Hi!
From my experience you can't do this. if you click the button they will get inside before any fight. And if you left them outside and they are defeated thy will retreat to another adjacent area.
In any case in my humble opinion you don't miss much because of this.
If the force is small they are better inside the fort/structure where the big enemy will not be able to put all his units in the fight at the same time because of the small frontage.
If you stack is big enough to battle it out in the open and teh enemy strong enough to defeat you most of the time is better for your army to escape to another area and survive to fight another day than to become trapped in a fort/city where it can be completely destroyed if defeated (defenders inside a structure cannot escape. They will fight to the death.
Fighting form inside a fort/city is a risky proposition. It have important defensive advantages (at least forts) but if they are defeated they will be completely destroyed and guns and wagons captured.
Maybe the better option is to put the big stack outside and a little garrison inside.
2- No, you must be doing something wrong.
If in a port, just stack the land units and the ships together and then order the fleet to move where you want to.
If you are boarding from the coast, drag the land units over the fleet and then order the fleet to move away. They should wait for the boarding before moving.
Also, when debarking its the same. You can order the land units to debark and the fleet to move away and the ships will wait for the land units to debark before moving.
Are you sure you are pointing right when drag and dropping?? do you see teh movement line marked on the map?
Be sure to not try to embark forces with higher weight than the ships transport allowance. They will not try the embarkation and will remain at land.
Regards!