I also don't have the luxury of having a bare roof this time since this roof was done recently....all though laid on top of another roof. This adds to the issues of laying the flashing on the roof. I worked the flashing into the shingles the best I could and will remove the top row and muck them down on top of the flashing. This should look OK and solve any of the leaking problems I've been having.
Next the starter course goes in along the roof line.
I need to finish wrapping, then I can finish the side shingles up to the roof, start the front and side corner a couple rows, and tie everything together when I get to the first uninterrupted row. And let's not forget - make a few more batches of shingles!