I don't remember offhand. One thing is an Orbit type waypoint using a non-standard mavlink message (which isn't defined anywhere except the code itself).
Basically you'd want to look at , where it parses MAVLINK_MSG_ID_MISSION_ITEM message and "translates" the contents to AQ waypoint types. So you just need to make sure the GCS mission planner is sending the correct data (and format) in the different message params (eg. loiter time, target radius, etc).
Also above that a bit, the MAVLINK_MSG_ID_MISSION_REQUEST is the reverse process -- this is where AQ sends information about the onboard mission back to the GCS.
Isn't the current APM MP based on QGC? Maybe you could bring the new/changed planner over to QGC_aq...
-Max