As Waresky stated, F6 Ships screen is the only way. FAC/Gunships functionally are just parasite ships within Aurora and currently don't have a flotilla/squadron assignment capability.
on Solar System MAp.8th from LEFT,icon are SHIPS,individual ships detail WINDOWS opened..on top RIGHT are a "MOTHERSHIPS ASSIGNED,check that if u FIND ur PDC's name..then ASSIGN'IT.
then on TASK GROUP windows are "retrieve Parassite" buttn on bottom..try that...next click "SET" button on top left and SHOW if ur Scout r joined on Task group:)
I don't normally build FACs but I decided to add a 1000 capacity hangar to my PDCs so I could assign a single FSC (Fast Scout Craft - no weapons, just enough range to intercept a contact and scan it before it gets near the colony).
Thing is, I can not find anyway of 'docking' the FAC inside the PDC - am I missing something? I can work with fighters fine!