I used Eternabond on the two outside trim strips on the roof of my Jayco before I found a leak. The roof was a one piece so there was no center seam to deal with, thankfully. But those outside edges need attention. That's why I did the Eternabond and never had to worry about it again. Get a good sealant (NOTHING from Home Depot or Lowes, etc) from an RV dealer or supplier online, something like Dicor. The silicone and other sealants at big box stores are not designed for the stresses and flexing of RVs and will fail in shorter periods of time. Surface prep, no matter what you use, is critical in getting a good seal.
Check the plywood for signs of actual damage beyond just being wet, namely, rot. It doesn't take long or much to ruin a good roof.
