We ended up doing out whole roof. I was going to try patching sections, but there was too much damage as I started to pick away at it. We had damage to the rafters, walls, and all the way down to the floor. If you have roof damage I'd prepare for additional water damage once you start the project.
As for cost, it depends on the size of the roof and materials you choose. I ended up going with Dicor TPO and purchased it for under $300 on Amazon. I haven't seen it that cheap since. You'll also need to account for glue, butyl tape, lap sealant, and wood.