With any HT system, the various different speakers (5.1, 6.1, etc.) need to be "calibrated" to a pre-defined level. You do this by outputting a test tone on the HT receiver and increasing/decreasing the volume for a particular speaker so it matches all of the other speakers output.
Since you will essentially be using an "external power amp" when using the HT bypass loop, your main L&R speakers are going to be powered by an amp that has a different output than the one powering your center channel and surrounds (internal amp in HT receiver).
Just be sure that you do this calibration after you set up the integrated amp/HT bypass because now your volumes will be different than they were before when you were using only the amps built into the HT receiver.
I've always used an analog Radio Shack SPL meter for adjusting the various channels. It is a bit more accurate than doing it by ear. However, my new HT receiver (Pioneer VSX-1014TX-K) has a nifty feature called mcacc that automatically does the calibration for me. It uses a microphone and outputs some very odd tones that it uses to calibrate the number of speaker, size of speakers, distance to speakers and output of speakers. Works perfectly every time!
Feel free to e-mail me directly if you need a better understanding of the HT bypass and calibration issue. It is really not very complicated once you understand how it works.