I don't worry much about this, other than my work badge is always in the same place and my extra gloves in the winter I always have near the top.

Otherwise I just jam crap in there. Been doing it like that for years now, no reason to change.

do you have a proper pannier rack? This is one with the extra support (dog leg) in the rear to keep the panniers from swining into your spokes. If not, you may need to pack both pretty full to keep them "in shape" on the rack. With a good rack designed for panniers you can pretty much use any panniers, packed however you want and not have problems.

BTW - I have baskets on one bike and panniers on the other. Both do the same task for me.