Using PSP(Paint Shop Pro) go to Mask >> Load From Alpha Channel, then after you load the Alpha Channel, go to Mask >> View Mask, then Mask >> Edit Mask. Now anything you make black in Edit Mask mode will become transparent (unless it's team color) or anything you make white will become opaque (to stop team color from showing thru).
Before you save the skin, go to Mask >> Save to Alpha Channel, double click on Alpha Channel 1, name the channel you are saving Alpha Channel 1, then save the skin as usual.