+1 on watch your settings !!! Boss (and most other) stompbox type effects are designed to recieve an instrument-level signal, not the line-level signal present at the FX loop. Keep the FX send on the amp around 1:00, turn the amp Output up to 11:00 or more, and use the Channel Masters to adjust your volume/balance. The lower Channel Master settings will help prevent overloading the pedal inputs.
FWIW I do it all the time (stompboxes in the loop) with my Triple and have had no probs overloading the pedals (Boss DD-6, RV-5). FX send @ 1:30, Output 12:00+, can get punishingly loud with the Ch Masters well below 12:00. IMO the amp sounds better like that (more Output, less Channel Master) even with the loop footswitched off.