Probably you already have her running now, but, ...I agree the designed position makes the stern planes very inneffective. The absolute best performance setup is like Bobs, because he's getting the thrust of water directly from the prop, and it is more effective right at the stern.
But! I do have to add that I have seen underwater footage of Dan Kachur's Nautilus in a swimming pool and that seems to be working perfectly with the 'as designed' configuration. Since the model is sailing quite slowly and gracefully in this video I conclude that the rear dive planes will
work as designed, but not as effeciently as ones placed actually at the stern. I think Dan's Nautilus was ballasted exactly neutral for that to happen. There's the rub.. often we are in a murky lake and can not see when neutral bouyancy is attained, and so we tend to sail slightly positive bouyant and drive the sub under dynamicly to overcome the remaining bouyancy. It follows that the more bouyancy your sub has the more dynamic force you will need to overcome it and drive her under.
To answer your actual question
..Rigging an APC to the 'as designed' rear dive planes will not be effective in keeping her level IMO unless
you are able to achieve near neutral bouyancy.