You have to add them manually - or use AI Flight Planner, available from Avsim, in which case you don't need AIFPC, as AI Flight Planner can save directly into FSX format.
I used AIFP to do the Wellingtons and one random DC-3 for Hixon and it didn't take very long at all - that was starting from scratch, not basing the file on an existing one.
Edit: Re-reading your post, it sounds like you want to just scan your aircraft directory, pick them and have them fly as AI. It doesn't work that way. You can create random flight plans for your traffic using the SDK, but they will be truly random. Otherwise you have to build your own flightplans for specific aircraft to/from specific places. You can do that in Lee Swordy's TrafficTools format and convert them using AIFPC, or can build them in AI Flight Planner. You can also do them through the SDK if you want, but any way you choose to build flightplans, they will not just happen - you have to create them.
Ian P.