The pedal you have (Digitech RP-90) includes amp and cab modelling, so one option would be to ignore the amp's preamp entirely, and run:
Guitar > RP-90 > FX Return > Power Amp
This is the setup suggested by the unit's manual:
Unfortunately, this means that the complex, multichannel preamp section of your amp ends up not contributing at all - just set it to clean and turn the FX mix all the way up.
The user manual includes the following signal path diagram, which shows the order the different effects are in and where the amp modelling sits:
Another option is to use only the effects up to and including the amp/distortion block (which you would set to either direct or one of the distortion pedals, not an amp and cab simulator), in the chain:
Guitar > RP-90 > Amp Input > Preamp > Power Amp
Or only the effects after that block, in the chain:
Guitar > Amp Input > Preamp > FX Send > RP-90 > FX Return > Power Amp
These options allow you to get fuller use out of your amp, but limit you* to one half or the other of the effects unit.
* By all means experiment with e.g. wah in the effect loop or reverb before the preamp, but effects generally sound "better" in the order Digitech suggest, particularly as a starting point.