Advice on Eternabond on my fiver roof

I have been working on my roof and found some holes I did not know were there. I got those repaired with Eternabond. I started working on the roof edge at the gutter line. I have been removing the old caulk that has finally started to come off.I have found a couple areas that the roof was cut short. I plan on running 6 in. Eternabond along the whole side.My question is, there is a 1/2 in. vinyl insert the whole way down covering the screws. Should I remove the vinyl insert and just cover over the screws or leave the vinyl insert in so it has a smooth surface to go over.I plan on running it down into almost the bottom of the gutter to have good adhesion.Thanks