Do not use Line-X.
I had one customer use a similar "flexible" bedliner.
Boat was junk. It cracked and came off in chunks. It would often rip off layers of hypalon with it, causing air leaks. It could not be removed to patch.
Use this instead : Inland Marine - Inflatable Boat Repair Products
If there are pinholes, patch them first. If there are seam leaks, I would advise using the internal latex sealant if you can.
Afterwards, spray the boat using their paint with an HVLP gun. Thin with water. Don't use a roller or brush...it goes on too thickly and looks blobby.