Well, I don't know how to set a 'piloet' :-), but to set as pilot:
1. Make sure you are at the same location as the other ship(s) you want to set as NPC piloted (must be the exact same type of ship as the one you are currently flying).
2. Go to ship inventory -> Manage piloted ships
3. Check the ship(s) that you want to control, and under 'select action', select 'set controlled'
4. Check 'Set NPC Controlled, and click the 'process' button.
Light speed is too slow! We're going to have to go right to...Ludicrous speed.
Amp Thane, Captain, BFF-1 class freighter EQUUS