You will probably need to cut the rubber roofing to do the repairs/replacement of the wood.
After you finish the repairs you can glue the rubber to the wood using the proper adhesive.
My recommendation is to use Eternabond tape to seal any cuts in the rubber. It will give you a long lasting and leak proof repair.
You can then cover the roof with the coating of your choice, if you wish. If the rubber is in good condition it may not need coated.
Dicor self leveling lap sealant is another choice to seal the cuts in the rubber. It would be a little less expensive than Eternabond. But it will not be a permanent repair.
I Use Eternabond on roof seams and edges.