Yes that is correct, in order for the switches 1,2,3 to match the amp channels 1,2,3.
M.A.G. switch 5 maps to the FX loop, and that had to be inverted also.
One further note about the FX Loop; I was getting excessive noise in general, and audible clicking / popping while changing channels, after checking cables and everything in the signal path (I'm using the GT10 in the 4 cable method), I discovered that the FX switch on the back of the amp did the trick. It needs to be pressed "IN" to the "O dBV" setting as opposed to the "OUT" or "-10 dBV" setting.
Thanks Again, feel free to contact me with any other questions.