I just added a couple of new panels to my setup last weekend, same idea. Don't worry too much about making holes in the roof, just make sure you caulk very well. I drilled holes, pumped in some Dicor self-levelling, placed the Z brackets (put some Dicor on the bottom of the bracket as well), then when the panels are in place, apply the self-levelling liberally. I took the opportunity to strip the old caulking off the existing panel and re-apply.
I will probably lay some Eternabond tape over each bracket, since I have some lying around.