I grafted on an HT setup to my 2-channel rig as well, pretty much the same way others have mentioned here. I have my pure 2-channel setup with my sources (arcam FMJ CD23 and a VPI HW-19Jr turntable) going directly into my preamp (audible illusions mod 3) which drives the 2 main channels. I use a cheapie Harmon Kardon refurb processor (AV230) as a surround processor; at the time, this was the cheapest receiver they sold with preouts on all channels. I feed my HT sources (LD player, cheapie Sony DVD/SACD, Windows media center PC, laptop, occasional Xbox) into the surround receiver. L and R preouts from the surround receiver go the preamp onto an unused input. Had to pick a volume setting on the preamp that was close to full volume and calibrate the channels on the surround receiver at that volume level and then always have to return to that volume level when running in surround mode.
I am also able to run SACD in surround or 3-channel mode (e.g. living stereo releases) for music, but it's not as purely direct as it could be since the L and R channels from my SACD/DVD go all into the surround receiver. Theoretically, I would feed the L + R directly from the SACD into my preamp as well, but I'd need to deal with coordinating volume levels between both systems.
regarding your sub question, personally, I only use my sub for HT duty as the LFE channel and not in 2-channel at all. A couple times, I have hooked up the sub for 2-channel use in parallel with the L and R channels (so did not use the line level crossover in the sub) by using another setup of outputs on my preamp.
Last thought is that since you are running a tube amp, you'll obviously also be using these amps to drive L + R channels for all HT duty as well so you'll shorten the life on them. Today, I'm running solid state amp, but my intent was to also move to VTL amps and preamps and I have that same concern.
Your setup must be very nice sounding. Looks like you've done a great job building a musical system. I think you're thinking the right thing by keeping your 2-channel setup as pure as possible and tacking on the HT onto that.