So if I were running 1 Small and 1 Medium Rail, should I go Feedback on the small and Super Pen on the medium or vice versa and why?
Secondly, if I can't imagine landind more than twice on a banking ship should I just go Super Pen on both?
If it's pve, I'd go medium feedback small super pen, but honestly, I've stopped using super pen. Landing 5 shots on the enemy PP (medium), or 7 (small, it's actually 7.5 but one hopes that your other weapons will hit the module a bit as well, so you'll likely get away with 7), simply takes just as long as destroying their hull with your primary weapons.
If PvP, you'll need to go both one or both the other. 1 small cascade won't be enough feedback to stop a cell and 1 small penetrator won't be enough to do module damage quick enough to make it not worth using your primary weapons on the hull. If you can fit one in, add a corrosive MC to amplify your hull damage and use two feedbacks, a medium and a small will work well.