For the rubber roof part, Eternabond is what is used to fix that type of repair.
The most important part of putting Eternabond down is getting the rubber prepped and cleaned proper before applying. Use either Eternaclean (works and smells like brake cleaner) or actetone. Both are high flash off solvents so they clean and then evaporate off quick.
Here is where I bought mine. This link is to the 4" wide roll. They also make 6" and 2"
EternaBond RoofSeal White 4" x 50'
On the inside ceiling, that one is cosmetic for the most part. Do what ever looks best to match your ceiling. It is not structrual at this point
Hope this helps
John
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2004 Sunline T310SR
2005 Ford F350 Lariat, V10 with 4.10
CC, Short Bed. Integrated Brake Controller
Reese HP trunnion bar hitch with HP DC