You should have a "Mix" knob on your Loop.
I think it's on the Left Side if you look at it from the back.
If you use Mod FX in front of the amp and time-based FX in the Loop, set the Mix knob to middle and adjust it to taste.
If you use all FX in the Loop, turn the Mix knob all the way up. This should turn the Loop into a Serial Loop.
Here is my setup:
Guitars:
2000 US Strat Deluxe, Ash body, Rosewood fretboard, Lace Hot Gold pickups, H-S-S
2004 US Strat Deluxe (2), Alder body, Maple fretboard, SCN pickups, S-1 switching, S-S-S
1997 PRS Custom 24, Mahogany body, Rosewood fretboard, Duncan Alnico II (Neck pickup), Duncan Custom 5 (Bridge pickup)
2005 Warmoth Soloist, Mahogany/Flame Maple body, Birdseye Maple neck, PRS Vintage Bass (Neck pickup), Fender SCN (Mid pickup), DiMarzio Megadrive (Bridge pickup)
Amps:
Mesa DC-2
Mesa DC-3
Setup:
Guitar___Boss TU-2 Tuner Pedal___Home made Solo Boost pedal___Morley Bad Horsie II Wah Pedal___Amp input___TC Electronics G-Major in the Loop with the Mix knob turned almost all the way up___Celestion Heritage speakers.
All of the guitars sound amazing through this setup, and I haven't even begun to explore all the tones I can get. I will have my hands full for the next 5 years.