[Q]

Unfortunately you cannot make a script for the AI how to use ships in SE IV. I hope this will be possible in SE V but in SE IV you only can make designs for the ships and instruct the AI to build these ships (vehicle construction file). If the AI has troop transports and population transports he will use them in SE IV. The troop transports work quite well, the population transports can however lead to unexpected results: depopulated homeworld, population transports loading and dropping population endlessly on the same planet. The main problem here in stock SE IV is that a single transport ship can load so much population that it will fill a small planet completely or load all but 1M population from that colony. Mods that increase the population mass will help here. Another possibility in stock SE IV is to give the AI only designs for small population transporters.