Personally, i put a very thin film of permatex (Red or Copper) on the muffler side and then make sure that i carefully mate the surfaces together squarely and the muffler doesn't slide around. In most cases you can hold the muffler off about 1/4" while you thread the bolts, then tighten the bolts 1 turn at a time.

I also put a smear of the permatex on the bolt threads instead of Loc Tite

This has always worked great for me.