welding body probs

[i heart square bodys]

okay so heres the deal, i think i ****ed up! i was cutting the center stake pockets out of my box , i cut the folds out that go around the hole but when i cut through it i noticed there are 2 layers of metal! i want to replace both layers as well as fill in the stake pockets, BUT i dont want to put 2 layers of metal together and then have moisture get in and bow out both pieces of metal as that will look like ass ! what do i do !