Cut out the roofing where it is soft, replace all rotted wood there. I used Liquid EPDM to repair my old Nash roof. The liquid EPDM gets "painted" on, for lack of better word, and forms a seamless repair, adhering to the existing EPDM roof (if that's what you have). Make sure to repair everything right the FIRST time, or else you will eventually be back in their a SECOND time.
Any wood that is soft or wet needs to be inspected and probably replaced. I would either cut out the rotted wood, or else use one of the epoxies meant to harden rotten wood. Then I would glue additional 2x2's to sister anything that is rotted. Replace the rotted roof decking, making sure to get all the rot out and replace it with good wood.
Its a pain in the neck, but it is something that can be a DIY project. When in doubt, replace it. Don't go in a second time. Good luck!
2015 Ram CTD
2015 Jayco 29QBS