Hmm,. not sure.
If you can make the low gain input's level the same as the high gain input, it shouldn't be a problem.
If your amp has an effects loop you could go with a little bit different setup.
Put a loopswitcher in there ( lehle Dloop is nice and affordable ).
Make a loop from
amp input to effectsloop out.
Another from rocktron input to output
connect looper to effects loop input ( in addition to any effects you have. )
So :
Loop 1 : Amp clean channel
Loop 2 : Rocktron device
Output : to effects like chorus, delay, whatnot to effects return.
Big plus is that the rocktron sound goes directly to the poweramp. Ofcourse, you could connect the chorus in loop 1 as well.