Aircraft that are imported are all placed in a generic subfleet. You will need to go and either add additional subfleets, or just rename this subfleet to whatever you want
All flights will be assigned to this subfleet. Unfortunately, you will need to re-assign the flights to be with the proper subfleet
Ranks are now assigned subfleets they are allowed to fly. This is different from the old version, which operated on a linear progression for the aircraft that are allowable per-rank. You will need to edit the ranks and set the subfleets that are assigned to them.