if bass is on channel 1, go into TotalMix pull the fader back on channel 1 for the input / output to your mains. You should still see signal on the input on channel 1 you just won't hear it. Go into Cubase and monitor your bass channel (may have to enable record, there may also be a "monitor" feature as well).
I do this all the time in PTs, StudioOne Pro, and ACID when recording my bass.
Now, you mention a modeller. You may have to place your modeller on the channel (as an insert/fx) in the software to hear the processed signal, you'll record the dry signal in this setup.
if your looking to record down the processed signal, then you would need to setup an input buss and have the modeller on the input side as an insert or fx.
I also use waves gtr standalone for practicing in the studio (vs. setting up my rig), the setup is the same in Total Mix, and then I monitor out of modeller to my mains.
I have never attempted to use GTR stand alone and route this output through to the inputs on the DAW, only because it isn't necessary, in my situation.
Hope this helps...