Okay, I'm going to give it a go here, answering some of your questions.
By the way, good eye noticing the city graphics, you can tell almost everything you need to know about a city by just looking at it. To add to what you put down, you can also tell if there is any industrialization by looking for the smokestacks and little factory graphic. The CS especially needs to pay attention to that because they have so few industrial areas to start, losing any is a big problem. This is also a good reason to try and keep your industrialization attempts behind the lines. Of course, with the Union able to pull off amphibious invasions, the front lines can be anywhere.
Someone already described the difference between reinforcements and replacements, but I'll emphasize that a bit. Replacements are what you need to flesh out depleted regiments, generally, the ideal is to have 10% of your total force available in replacements. You can see the numbers on the replacements screen. It tells you how many replacement "points" you have, and the max number you can have. So you generally want to try and keep 10% of the big number in stock. Not always possible, and after a bit of playing, you'll find out which types you need to invest more in. Generally for me, I tend to go through field arty and cavalry at a pretty high pace, so I try and keep those numbers up, and of course, line infantry are always the big one.
Reinforcements are the new units you'll need to increase the power and size of your armies, and garrison your rear areas. Units take time to train, and it's proportionate to the size and power of the unit. So, militia will raise and be fully trained by the following turn, while most regular units will take two or more turns to fully train. Keep this in mind when deciding what state to build units in, because while untrained units can defend themselves, their power will be significantly reduced. Naval and HQ units take quite a long time to build, so you need to plan in advance for these.
You'll notice that most units require three things; money, conscript companies, and war supplies. For the South, the big limiting factors are money and war supplies. War supply production can be increased through industrialization, but it's expensive, so it's a trade off whether to try and increase your industry or hope to depend on blockade runners to make up your shortfall. Blockade runners will bring in either money or war supplies, depending on which you need more.
The draft screen is pretty simple. Remember on most of the screens like this, you can right or left click on the description text for the options to cycle between different options for each. For instance, on the drafts screen, you can choose to call for volunteers with; no bonus or with a $1,000, $2,000, or $3,000 bonus. Generally, the US is the only side that will be able to afford to pay for volunteers. The CS money situation is just too tight to pay for it. The number of companies you get depends on your current VP I believe, so the more you have, the more recruits you'll receive. The other side is the draft options. You can choose Partial or Full mobilization to significantly increase the number of conscript companies available to build reinforcements and replacements. Usually, you'll want to start by calling for volunteers as there are no penalties for this option. Later, as you need more units and have built up your VP and NM, you can afford to take the hit to each for calling for a draft. Remember though, you can only use each option once every 6 months, so choose carefully.
The Financials screen is a big one for both sides. Nothing happens without money. The CS can't be afraid to let their inflation creep up. Everything will cost more, but without the large infusions of money available, the war will be lost. Inflation will also slowly drop over time, so if you can get to the point where you don't need as much money, you can use the lower end options and prices will slowly return to normal. The first two options you should look to use are the taxes and bonds. These impact your NM and VP levels, but don't have as large an effect on your inflation level. You can choose between 5, 6, and 8% war bonds, increasing the % will bring in more money, but will increase the penalties naturally. For the taxes, you can choose limited exceptional taxes, income tax, or regular exceptional tax. The same applies here, with limited exceptional providing the least money and fewest penalties up to the regular exceptional providing the most and costing the most. Paper money printing should be the option of last resort. It will provide a large infusion of money, but also increases your inflation by 4% per use. The one advantage of this one over the other two is that it can be used at any time, whenever you need a quick shot of cash. The other two are under the same 6 month limitation as the draft options.
Industrial expansion is a bit like rolling for tech in Axis and Allies for those of you who played it. In other words, it's a calculated risk. You can invest in it in the hope of increasing your production of the three types of supply, but it's not guaranteed, and it is expensive. I've seen 3 or 4 different industries get built in one turn, and I've had many turns where nothing gets built. It's relatively more important for the CS than the US. The US starts with a strong industrial base, and can probably make it through the war without any investment. The CS is quite lacking in supplies, so increasing the industry level can make a huge difference. You'll gain more if you can afford to keep a steady level of industrialization than if you are continually shuffling or removing the funding, so it's advised to scrimp and save as the CS to try to keep at least a light level of funding in at least one state. If you are successful, you'll receive a message the next turn, telling you where the attempt succeeded and what and how much you increased your levels. The other option here is the rolling stock and steamship investment. Keeping your rail levels above 100 is something to try for as the CS. Not only does it significantly improve the movement of supplies to the front line troops, but it gives you a margin of error if you have to do a significant number of rail moves in any turn. If you can manage to stabilize the economy, further investment here is never wasted money. Steamships work generally the same, but are, naturally, limited to river movement and supply. This option has a much larger impact in the west than the east, so rail is generally more important since it's usable anywhere you have a rail line.
You're correct about the loyalty levels, they are regionally (actually county) based. The loyalty page here is just for mass changes. If the Union takes an entire state, for example Louisiana or Mississippi, quickly, then you can use this screen to attempt to quell statewide unrest quickly. For more regional or local changes, you'll use garrisons, generals, and armies to affect the levels. (Hint, generals with an occupation trait like Butler increase your levels significantly faster.)
The political options screen is pretty useful. Move capitol is obvious. You can choose one of three cities to move it to, and believe me, moving it is much preferable to losing it, so if you think it might fall, use this option. The bottom left option is the foreign intervention option. Here you can cycle between three choices to attempt to increase (Or decrease if playing the US) the chances of foreign intervention. The first option for both sides is the "tough" policy. Either a blockade or an embargo on cotton. This is a high risk, high reward option. The level can move significantly, but it could swing either way. The next two are the concession options. You can choose territorial or trade concessions. These are unpopular with your people, but can be useful. For the CS, the trade concession one can be quite handy since you receive money for choosing it. The change level is quite a bit smaller than the tough option though. The right side options are not available at the start, but will appear eventually. The top right is a prisoner exchange, which will increase both sides conscript pool. This obviously helps the CS more than the US since they're working with a much smaller pool, but can get the US through a tough spot now and then too. The bottom right is the emancipation policy for both sides. If you choose emancipation, you will also have the option to recruit blacks on the draft screen too.
The objectives screen is nice as it shows you the current foreign intervention level, victory level, number of POWs and other useful information.
The blank generals are simply those who's artwork is not done yet. This should be remidied through a patch soon.
The blockade level is related to the number of blockade ships the US places in that box to attempt to stop your blockade runners. The US can do two blockade types, blue and brown water. The blue water uses the ocean boxes and attempts to find and destroy your runners, while the brown water is a close blockade of ports by placing a certain number of ships directly by your harbors. This is much more effective, but also more dangerous for the US ships.
Army of the Potomac was indeed the initial (Optimistic) name for the CS army in Virginia. Lee renamed it when he took command.
When your resources go into the red, the final purchase or purchases that made it go into the red will not be built. If I recall correctly, the builds are saved and done the next round, but I can't recall off the top of my head, I usually keep my stocks in the black at all times.
The initial division HQs you created were placed in Montgomery because those units are produced in the capitol, and in the beginning of the game, the capitol is in Montgomery, then moves to Richmond on the historical date that they shifted their government.
As the engine is currently, they were unable to duplicate the whole West Virginia secceeding from Virginia and joining the Union thing, so it begins as a US state. Limitations of the game there.
The capture of Norfolk netted the CS about 2,000 naval guns and literally tons of supplies. Those supplies enabled the laying down of those CS ironclads. Be warned though, ironclads are, in my opinion, significantly underpowered still. I've brought this up in the beta forum, and I think they said it might change, but they are definitely not a fix all for the navy, even against wooden ships.