You need to check the specs for whatever specific manufacturer you're using but here are some quick answers-
I like iso underlayment, attached with plates and screws. then you don't need to worry about nail holes, although you can attach directly to plywood and I don't think nail holes are an issue. Valley and other seams need to be pretty tight, but I would install Reinforcing strip over it to help bridge the transition. I usually finish both my rakes and eaves by running epdm long over the edge, installing drip over top, prime and tape. Its quickest and effective.
But there are many details.