Think of a dart (like with a dartboard), most of the mass is in the front. This causes the center of mass to be shifted forward, and things rotate around a point that's not in the center. If you drop the projectile without any angular momentum, it'll start rotating so that the heavy bit goes down. I think. I don't know if that's necessary for your projectile or not. You can play with the settings once you've got it set up.

You can rotate the entire composite with rotateByAngle or rotateByRadian.
http://www.cove.org/ape/docs/api/

I think you'll have to move one or both of the internal particles in order to place the whole thing where you want it.