Should I fill nail holes in a roof deck before installing underlayment

That's at the PEAK of a shed roof, true? If that's the case, what you have amounts to a ridge cap, but nobody I know of manufactures premade ridge caps for shed roofs (too many different possibilities, not enough market), so the builder used "drip edge" or flat flashing (bent around the peak) to function as a ridge cap.

There really aren't very many good alternatives to that situation, so what they did is actually pretty common on the peaks of shed roofs. They really SHOULD have tarred over the nail heads, though.

1. The new felt should go under the old felt.

2. The new flashing should go under the old felt and over the new felt and new roll roofing.

3. Depends on the slope of the new roof. The lower the slope the further it should extend.

4. Roofing nails to the existing structural sheathing.

The big idea is that layers of the lower roof should sit below corresponding layers of the upper roof. That is:

• Everything should lap just like shingles.

• Nothing should back-lap.

• The flashing should double lap the roll roofing.

• Even though the higher roof was installed first, the end result must be the same as if you started at the eave and worked all the way to the ridge.