stuck in a quandry -what's best solely on quality?

Ok - here's my situation. I have the bug. I have budget constraints. Currently running Denon AVR-3300, with an Odyssey Stratos covering the front right and left amp duties. Looking now to purchase a second power amp to handle the center and surrounds, allowing me to ditch the receiver (which has treated me very well, and kicks butt for theater, just not 2 channel). Once the second amp is in, I can buy a new processor that handles a center rear channel or 2. Current budget is $1000. The question is should I....

1. buy a 3 channel, such as a Chiro C-300, which is currently available, and save some cash for the processor and get it sooner? (140 x 3 @ 8ohms)

2. buy a 6 channel such as the Parasound HCA-806, that I can run in 5 channel mode - bridge 2 channels for the center and have 4 more channels for current rears with 2 dormant channels until processor and rear speakers come, also saving some cash for processor? (180 x 1 bridged @ 8ohms and 80 x 4 @ 8ohms)

3. or spend the $$$ and buy a Citation 7.1, which I can bridge for center and unbridge down the line for a single rear center? (150 x 4 @ 8ohms or 1 x 450 and 2 x 150 @ 8ohms)

suggestions with reasoning behind them would be VERY welcome.
I'd keep the Stratos powering the front 2 channels, buy a relatively inexpensive Denon receiver(or similar) with preamp outs to handle processing and power for center/surrounds, and put your money into a high-quality stereo preamp for critical 2-channel listening. Hook the front L/R preamp out from the receiver to any line-level input on the stereo preamp(or the tape loop) and you're good to go(you'll have to volume match the stereo pre for surround/movies unless it has a home theater pass-through option). This way you maximize critical 2-channel sound quality(I'm assuming since you bought the Odyssey you care more about stereo performance) and minimize the expense on the other areas that may be less critical to you and that you may need/want to change again as surround formats continue to evolve(as opposed to blowing big $$$ on a pre/pro that probably won't sound as good as a quality stereo preamp and may or may not be truly upgradable for future formats). Best of luck.

how does a home theater pass through work?

if my cd player has analog outs, i could run them to a stereo pre-amp and run the digital connection to the receiver....but then how do i get power to the speakers from the receiver through the stratos? run the pre-outs of the receiver through the pre-amp as well, and set the pre-amp for pass thru? so that way, the pre-amp needs at least two inputs, one of which is a pass thru, and all front end would go thru the pre amp? this could be a great solution! there are pre-amps that do this?

You pretty much hit the nail on the head. A lot of stereo preamps these days have a "video" input that you can use for this purpose, but any line-level input will work and you're right that the preamp will need at least two inputs(or one input and a tape loop) for this to work. And yes, the stereo preamp will be the only thing running into the Stratos(the whole point of this is to have only high-quality stereo components handling the signal for 2-channel listening)

The only limitation with this(if the preamp doesn't have an HT pass-through feature) is that when you set the volume levels for all the speakers with the A/V receiver you'll need to have one reference point on the stereo preamp(say halfway) so when you switch to surround everything remains in balance. Some stereo preamps(see below) feature an HT pass-through(generally assigned to one of the line-level inputs) which essentially takes the stereo preamp's volume control out of the circuit allowing the A/V receiver or pre/pro total control over the volume(i.e. no need to set a reference level on the stereo preamp--it just passes the signal through from the receiver to the amp, hence the name HT pass-through). If you have a wife/kids/roommates that also use your system the HT pass-through is nice to have, otherwise it's just a convenience thing(although you'll have lots more choices if you don't need the HT pass-through feature).

Some manufacturers that offer an HT pass-through: ARC, BAT, Sonic Frontiers, Rogue, Conrad-Johnson, VAC, McCormack(RLD-1), Proceed/Levinson, Adcom(GFP-750), and a few others I can't think of right now.

With this type of setup you're likely to save some money, get better stereo sound, have better upgrade flexibility, and have less $$$ at risk as surround formats evolve. If you care mostly about 2-channel and don't necessarily need state-of-the-art home theater performance I think this is an optimal setup. Best of luck.

If you like the stratos, why not get another stratos amp? I believe that would be a better solution than the other amps you have listed.
I agree with the other posters, a pre-amp with HT bypass is the way to go. The amps in your AVR-3300 are plenty good enough for center and surround speakers. They are not as critical as the mains. I went through the same process as you fairly recently. Almost two years ago I decided to simplify things and bought a Denon AVR-5800 to base my system around. It's great for movies, but it didn't take long before I wanted better two channel performance. Now I have a Rowland Synergy IIi pre-amp (with HT bypass), a Rowland Model 10 power amp for the mains, and only use the AVR-5800 for home theater, using its internal amps for the surrounds (I don't have a center). This system sounds great in two-channel AND HT modes. If I had to do it again I wouldn't have spent as much on the receiver. Some may disagree with me, but I think its silly to spend megabucks on surround channel speakers and amplification. The information in those channels is mainly sound effects which doesn't require the ultimate in quality to be effective.