I have a JJlabs Thunder 2x75 Mark II and 4x12 cab and my friend's BOSS Metal Zone I just recently hooked up. What's bothering me is that connecting the pedal to the effectsloop sounds so much better than to the regular input on the amp. With this approach I can't switch on the amps built-in distortion AND the clean channel is somewhat less clear with the guitar passed through the Metal Zone. Are there any way I can keep the "better" sound of the Metal Zone when connected to the Return and be able to toggle the amps two channels (dist and clean)? Any tips, thoughts or cash are welcome.

Thank you for your time.