I know what you mean, you want to switch the amp channels from your multi-effect unit, so in case you want to use the amp's distortion you won't have to step on two pedals at once (the amp's footswitch & the multi-effect).

Actualy I've never heard about this cool feature before in a multi-effect unit, I don't know if the GT-6 have it, but it's not on my GT-3 .

Anyway, usualy people who uses a multi-effect units like these you mentioned plug it directly into the amp's clean channel & do the rest from the unit.

You can always get a custom pedal board to do this ... if you can afford the extra $$$. ;)