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The previous owner of my MH nailed down a piece of tar paper over a section of the roof, I removed and coated the roof last fall, but now the nail holes are open is there a fix for these holes, I was going to Caulk them but caulk doesn't last long, is there something better ??

If this is a metal roof, you could put a dab of caulk on the hole and then drive a screw into it. Then put a good dollop of caulk around and over the screw. The most important part is cleaning. You could even use sand paper to get any crust or oxidation off of the spot. I would then wipe the spot clean with lacquer thinner. Then do the screw. Done well, it should outlast your regular re-coat maintenance.

JD the screw thing is a good idea but I forgot to mention that they nailed the nails through the metal and into nothing there was no wood under where they nailed...

You could use a stainless steel rivet instead but I think a #10x1/2" (5/16x1/2) hex screw would seal the hole up with just a dab of polyurethane sealant under the screw and then sealed over the screw.
You could use http://www.mobilehomerepair.com/stickit.php from the parts store. I use Eternabond a lot and have never had a problem with it. The surface must be clean and apply with pressure. A rubber roller is best. The tape should outlast a good coating.
The hole will need maintenance like the rest of the roof. If a hole does not seal up, it is probably a problem with the surface, like the surface is not clean enough, too much rust, using aluminum with galvanized steel, etc..