Generally the modeler output is run into the effect loop of the tube amp thereby bypassing the preamp section of the amp. Doing this insures that little coloration comes from the amp's preamp and the modeled sounds will remain true. However, you are still going to get a bit of flavor from the tube amp just because it still has some of its own character, but bypassing the preamp and tone stacks will provide the least coloration and the modeler will more effectively model.
If you don't have an effect loop on your amp then turn down the output on the modeler completely and fully turn up the master volume on the amp and the channel input that you will be plugging the modeler into. This should get the truest sound from the modeler in this case. Slowly bring up the modeler output until you get the desired volume.