When I patch tubes with store-bought patches, I read the tiny print that tells you how that particular kit is supposed to be applied. Patches from K-mart are elcheapo (made by Bell, I think), come in sort of flimsy sheets, are applied with the (hmmm, can't remember which) side down (I'd have to read the directions). They curl like crazy when the glue hits 'em, so I generally weight the whole mess down with a telephone book until it has a chance to dry. Those cheap patches work fine and go farther (cause you can cut 'em to a size that suits you).
The brand I buy at the bike shop has an orange side that is supposed to go down (against the tube). They have a nice taper and make a smooth patch (as if that's necessary - you'd have to patch with a brick or be a princess (and the pea) to actually feel the a road difference between these two types of patches). But, they do make a nice patch.
My guess is that if you put either type on backwards (or upside down), you are still using cement designed to make rubber "melt" into rubber, and once that happens, the patch will be strong - just as strong as if you had put the patch on "correctly." I would not worry about it. Chances are, whatever caused your flat will cause another one somewhere else on the tube long before a patch job will fail.
Caruso