you wold usually only move one ship at the time, they could even be in diffrent sectors. they would share their scrap supply, but not the other resources. If you meet in one sector, you would be able to exchange crew, supplies, wheapons etc.. if one ship dies, its lost, if you were in the same galaxy, there would be an event where you gather the ships remainings. If both ships die, you failed to earn the species trust and you won't be able to get their boni or hire their species. Also, you should only use the kestrals for basedefense, the federationcruisers would be searching for the scientists that invented the artillery beam. for the support ships i mentioned, there should only be six, not twenty. You would be able to buy stuff like cloaking for them and programm your own ai for them. there would be some presets, like a boarder strategy and so on, but you will have the option to decide completly on your own, if you take the time, for example when to cloak, when to shoot, what to do if systems get dameged and so on. you could save these strategies and build identical ships next time, wich would use the same ai.