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@ Riveros: normally your best soldiers will attack. If you click on an enemy building, you can choose whether you would like to attack with your strongest or your weakest soldiers. It's on strongest by default. But perhaps you're attacking a building nearest to one of your military buildings with weak units. If your building with stronger soldiers is further away, then it's possible that your weaker units attack.

There is a way to swap soldiers. In the military menu, you can choose the strength of soldiers garrisoning your buildings. If you have a guardhouse with a general and a private, and you conquer a building in such a way that your border is extended far enough that you don't need 3 soldiers in that guardhouse anymore, normally the general would stay there. But if you pull the right bar in the military menu all the way to the left, a private will stay.

However, you can't say: in that building I want generals, and in that other building I want privates. If you finish building a military building, a soldier in a storehouse/HQ nearest to that building will occupy it.