I have a GT-100 and I know what you are getting at. As you describe what is going on and the parameters involved, you've shown you aren't a mornon!! :).

The ideal situation would be if you could go into manual mode (where you can turn effects on/off via the footswitches) and assign a footswitch to the S/R "effect". I don't know that you can do that, but I wouldn't be surprised if there was some clever way to make it happen. If nobody can provide the answer here, maybe you could find an answer in the BOSS forums.

Another approach you can take is to create your patch with everything you want with the preamp engaged (S/R on). Then make a copy of it to another patch in the same bank. In this patch, disengage the preamp (S/R off). Switch between the two patches to engage your amp's preamp or use the preamp in the GT-100. Be careful about levels though!! When your amp's preamp, the volume is completely controlled by the GT-100.