Se what good pictures do.
Yup take it down to the plywood and change what you need to. The instructions for roofing are on the package. But I agree with the roofin god, the issue looks like it is the wall flashing on the chimney. Or the area above is leaking from somewhere else.
I would remove a piece of siding above this area to make sure the building paper(if any) is not tucked behind the flashing.
Kind of like tucking your raincoat into your pants...you get wet.
Be careful up there with bad structure, many folks fall in, or off.