Not exactly sure if this is the answer your looking for but here goes;
4 cable method
1) Back of Gt 100 output R === connect to effects loop return on your amp
2) Back of Gt 100 ext loop send === connects to the input on the front of your amp
3) Back of GT 100 ext loop return === connects to back of amp effects loop send
4) Back of Gt 100 input ===Hooks to Guitar
so now everything in the chain that shows up before the send/receive in the chain on your GT 100 window, and if the send/receive is on, gets sent through the front of your amp.... which allows you to use the EQ on your amp for tone control.
without the send/receive being set to the on position in the GT chain, everything goes through your effects loop on the back and makes the GT 100 your complete control.
The best way to use the amp sims..... imo.... is to turn everything in the chain on the GT 100 to off, except for the preamp simulation you want to use, and run it through the effects loop not the front of the amp otherwise your using the tone control in your amp. Sometimes noise gates or eq's help when left on in the chain.