shawn,
first thing is see if you can find someone that can help you tune your engine. i know you dont belong to a club but you cant let 1 bad experience keep you from meeting a good group of people who can and will help you fly. now with that said see the below
yes it does matter what line goes to the muffler if you have it hooked up to the in tank line that goes to the bottom, that is the fill line and if you have it hooked to the muffler you will be adding air bubbles to the tank (back presure from the muffler) .
you want it hooked to the line that curves to the top of the tank. also if you are using a plug to plug the fill line off make sure it is sealing good and not sucking air.
bassman