I use Project AI for all my AI needs. Yes, you can get rid of the default traffic, too.

I found a program not long ago that makes adding your own traffic stuff a piece of cake.  Its called Traffic Wizard and it can either be found here (I think!) or at avsim.com.  It requires Traffic Tools (by Lee Swordy), but makes a great UI that takes away all the need for sorting through page after page of stuff to find the info you need.  You'll still need to read up on TT, but it should make things a little easier.

I would also make a suggestion about editing the files:  Instead of adding aircraft to the list TTools makes, try just replacing the existing entries with the aircraft you want to have at the airports.  That way, you don't have to go into the flightplans and delete dozens of lines of code.