You can find a guide on how to plan a GPS waypoint flight with arducopter here - Arducopter Quickstart Guides and Tips - Arduino based Arducopter UAV, the open source multi-rotor
As for mounting your GPS/Compass for the best performance you can see this post
Its important to do an initial compass calibration before flight, this is done on hte first time setup on the mission planner software.
Or you can see this video
