If you're saying what I think you're saying, I don't think it matters that much. By the time you are sanding, etc., you should not be able to see the glue. That's what I have read anyways. Shouldn't make a difference in the long run. Some parts of my helmet are literally caked in hot glue.
I agree with the others but you should work on keeping it clean. The keep any exterior 'bumps' to a minimum and sand or cut them off before the resin process. The cleaner your glued pep file is the less work you do in the sanding stage. Good luck and post some pics because even though you may be embarrassed it helps with the critique process. Learn from your mistakes but don't worry you can fix anything with this method. Believe me, I have fixed some bad pep files before.