First off, it doesn't make a bit of sense to use amp modeling to change the entire tone of an already great sounding amp. Secondly, it was more cost effective than buying a ton of pedals to get the effects I wanted. Third, just because I don't use the modeling on my tube amp it doesn't automatically mean I don't use the modeling in other situations.
That being said, as far as hooking everything up correctly, I've followed the diagrams that can easily be found via Google, so that's likely not the cause. But thanks for offering your opinion, with no obvious solution. It was quite helpful of you, and very generous to take time out of your life to offer up absolutely nothing.