When using a guitar amp, you really need to plug your amp modeler into the effects return instead of the regular input jack. A guitar amp can basically be divided into two parts (without getting too technical)... The preamp and the power amp. In a tube amp, the greater portion of your tone will come from the preamp (where all the tone controlls and gain controlls are), but it will also be colored by the power amp section. This will be dependant on what type of tubes you use, and how hard you push the amp. A solid state's power amp section, on the other hand, won't color the sound much, if any, at all. When you plug into the effects return, you are bypassing the amps preamp. So, the only coloration you will have then will be from what little the power amp might cause and the speakers you play through.

The speakers you use will have a large effect on your overall tone as well. With a modeler, I would choose a speaker that wasn't too hyped in any particular part of the frequency range. Here's an example: Celestion Vintage 30's are hyped in the mid and hi-mid range. This causes their punchy and in-you-face tone. Celestion G12T-75's (stock in the newer Marshall 1960a cabs) have the mids scooped a bit, and the highs and lows hyped a bit. This makes them good for modern metal tones. I would probably use a speaker like the Eminence Wizard. This speaker has a fairly open tone to it, which covers the whole range of the guitar very well. A speaker like this will tend to work better with a wider variety of tones than a speaker like the Vintage 30.

I hope some of this helped out without getting too confusing :o