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...

i'm using cubase 6 to record bass but for some reason i can't turn the bass input signal off so it hears thru when i use an amp modeler

i can't find where to turn this off

can anyone care to assist in this, thank you