To move an NPC, you must add it to your party. Then it will follow you wherever you go. As for making them fly, someone else might be able to answer that.
If you have multiple fighters of the same type, there is an option under Manage Piloted Ships to set them NPC Controlled. This means the ships will automatically follow yours around, assuming they are all initially at the same location and the ship you are piloting is the same type as the NPC controlled ones.
However, you do not need to actually have an NPC on board any of the ships to do this, and pilot NPCs do not do anything at all yet.