The best way to get good tone with a modeller-to-amp setup is to run it through the effects loop or, if available, through the preamp bypass input of the amp. Running it in front of the amp, unfortunately, compromises the tone as you're basically running the pre-amped and processed tone from the modeller through another preamp.
Even though some modellers have an amp/line switch, these things are still primarily designed for direct recording use.