Can I use a pre amp with a receiver

If your "auxiliary amp out" is in reality a line level out you should have no problem. I have a B&K 307 but it only powers the surrounds, rear and center. I use the line level outs for the l/r to feed a Rouge 99. When I watch tv or a dvd I set the Rogue at a pre-defined level and use the b&k for volume control for the whole system. You don't really need an HT bypass, matter of fact if your l/r amp has too much or too little power you may find tuning the volume for ht through the integra, or any av receiver, difficult if not impossible because with a bypass you cannot increase/decrease the volume to your l/r speakers independently of your integra.

I think what you want to do is get a pre-amp with HT or cinema bypass. Run a search here on the Home theater bypass and you should find some threads that give you more detail. If the Integra has pre-amp out for each channel then you should not use that as an input for your pre-amp.