I figured I would go with the "upside down martini cut in the wrap" method. I have aluminum windows.
I found this:
It looks like it will work pretty well, and seems to be the norm.
I don't have the premade sill pieces I have seen in several examples so I am going to have to make my sills out of flashing. I'm sure this can be done but I'm not sure how to do it correctly. I notice most people do it with the tyvek flex wrap stuff, but all I have is regular adhesive backed flashing. I picked up a roll of 4" wide and a roll of 6" wide.
I also found this, which kind of contradicts the normal method a little but makes some sense..