You can apply "oil" based polyurethane over "oil" based enamel, you can also apply "water" based polyurethane over "water" based enamel, never mix the two, there's to much of a chance for problems.
The best solution (fastest and most durable) for protecting woods, is to use the old masters technique: apply 3 to 10+ very thin coats of glossy waterborne polyurethane (also called polyacrylic) and...
If the damaged area is small then a skrim or jointing tape can be used, if the damaged area is large then it must be cut back to the joists, replaced, jointing tape applied then skimmed.
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