The only way I've ever seen work is the one the MAIW team use, which I've adapted a couple of times for use on other fields. The short version is that you create a fake airport, with a zero-length runway, at whatever altitude you want, and set it to whatever lat/long you want your waypoint at. Then, when you create the flightplan, you set it to TNG. If you set the time between the TNG and setting off for the next airport to less than 20 minutes, the AI should, in theory, hit the waypoint, think "nope, not enough time to land here", and head off for the next airport/waypoint.
So, using KBOS as our initial setup...
1. Create waypoint airport, and call it something like KBO1
2. Set it to wherever you want the waypoint for the flight out of KBOS.
3. Create the flightplan to leave KBOS, fly to KBO1, do TNG for 15 minutes, and then return to KBOS.
I do have to note some things, for clarity's sake:
-This was all done in FS9, and I've never had the chance to try it out in FSX. It hasn't worked everytime for me, but it has more often than not.
-The AI will generally hit the waypoint as a "missed approach", so the AI will drop its gear and act as though it's about to land on nothingness. At some point, it will pull up, retract the gear, and head on its merry way. That, unfortunately, is a limitation of the FS AI engine.
-You could use an already existing airport as a waypoint, but the AI will then drop down into the pattern, and fly a missed approach on said airport, which would look quite strange if you are, for example, setting a fighter patrol pattern at 20,000ft.
Hope that helped at least a little. You might want to drop a line to the MAIW crew, and see if they can give you a clearer walkthrough on the waypoint system.
