Ok, let me get this strait.
You painted the car base/clear and the bast turned out ok but the clear didnt?
If so, depending on what acctually i wrong with it ( runs, sags, dry spray, orange peel, dirt....ect) you will likely be able to water sand and polish it smooth. BUT if yo ualready have the gun and clear it might be easyer to simply sand the clear smooth again and reclear it with a single coat (if you dont "burn through") if you burn through when sanding it, it will requier that some more base be sprayed in that spot before the clear is applied.
hope this helps, if not keep the questions coming