Footprints:
- Zero? Sure.
- One? Good.
- Two? Nice.
- Three? Great.
- Four? Bomb-proof!
My point is this: if you have a waterproof floor on your tent, you don't need any footprint. The trouble is, you are subjecting your tent floor to the abuses of rocks, sticks, sea-shells, brambles, or whatnot - meaning it will quickly get micro-tears and perforations.
Enter the footprint: a cheaper, replaceable protector for your tent floor. Thus, you want to put it OUTSIDE to protect the floor of your tent, which is (or should be) waterproof already. The footprint itself is usually waterproof (and in fact. some tents can be set up with just to footprint and the rain-fly as an ultra-light body-less option.)
Now, if both your footprint AND your tent have lots of wear and holes, then neither will help much (even together) in a deluge. Sure, ANOTHER footprint inside would help (assuming it is structurally sound) but if you need it, you might re-consider how your floor got to this state of disrepair in the first place, and re-adjust accordingly.