Matt,
Good questions! I've posted this once or twice before but this is a good area for a repost. Many people will tell you that in order to integrate the two you'll need a 2 channel preamp with HT bypass/pass thru/whatever they are calling it. Basically what that is is a separate set of inputs on the preamp that passes directly to the output of the preamp without going through any processing, amplification, tone, balance or volume controls. This way, you run the mains output from the pre/pro right to the bypass of the 2 channel pre and the pre/pro controls everything. You do get the best of both worlds this way, however, your choices are pretty limited when it comes to 2 channel preamps with this option. The way I'm doing it you can use ANY preamp and amp combo for 2 channel as long as the preamp has more than one input!
People might ask the question - what's the need to begin with? Well, long years ago when I just got out of high school I picked up a kick ass (for me) 2 channel rig - B&K amp, Superphon preamp and Polk RTA11t speakers. I was always interested in (at the time) Pro Logic and tried it but it just wasn't ready yet. Within the last three years we decided Digital HT was for us and I sold the amp and preamp to fund the purchase of an HTB. Theater was excellent and everything we hoped, but two channel sucked. Since then it's been my goal to integrate the two into one system that does both. We've got no space for two separate systems.
I think over the last two years I've gotten very close and am one speaker upgrade away from being very happy with things. I just placed an order with Klaus for a pair of Lorelei's and a Nemesis center to replace my polks and the CS400i center I've currently got. From my experience I think you really can integrate the two and get the best of both worlds. I love my Philly Audio Blues preamp, but it doesn't have pass thru so this is the way I've got stuff set up:
When I listen two channel, it's PURE two channel and when it's theater time it's pure 7.1 Home theater. I took the pre outs for my main L&R out of the Denon (pre/pro) and ran them into the Philly preamp (2 channel) DVD input. Then when I calibrated the home theater system I noted where the volume on the Philly was and marked it with a small piece of tape. Now, when I watch a movie, I just switch to DVD on the Philly, turn the volume to the marked spot so that the volume gets set at the appropriate level and listen to a completely balanced and calibrated 7.1 system!
It goes like this connection wise:
Two Channel
Source - Sony DVP-S7700
Cable - HDXV Digital
DAC - Scott Nixon Tubedac
Cable - Groneberg TS Premium
Pre - Philly Audio Blues 7b - (connected to the CD input)
Cable - Triphazer line level 20
Amp - Odyssey Stratos Stereo Extreme
Cable - TS Premium
Speaker - Polk RTA 11TL
Home Theater or TV
Source - Panny DVD player or Sat Box
Cable - Nixon Digital Cable
Processor - Denon 3802
Cable - Stealth ETS
Pre - Philly Audio Blues 7b - (connected to the DVD input)
Cable - Triphazer line level 20 & Stealth ETS
Amp - Stratos for Mains and Newcastle AM9080 for center and side surrounds
Speakers - Polks, CS400i center, f/x 500i side surrounds, RT25i rear surrounds, SVS CS-2039 w/ 250watt plate amp.
The only issue then is that your Digital Receiver or Pre/Pro HAS to have pre-outs for at least the L&R Main channels. Typically, if it has pre-outs for the mains it has it for all the channels.
Unless you do a lot of 5 channel music I don't think it's THAT important to match surrounds and the front three. The front three are important to match however and that's why I went all Odyssey.
PM me if you have any questions or want to discuss further and good luck!
Brian.