combining 3 channel and 2 channel amps

What's the best way to utilize a three channel and a two chammel amp for HT? I just got an Aragon 8008x3 and an 8008st. Is it better to use the three channel for the fronts and center(Aragon talks on its website and in reviews about the 8008x3 intentionally not being a triple mono so that power can be shared from one speaker to the other as sound effects move across) or will the two channel amp sound better and provide better two channel performance? Any advice appreciated.
You pose a very interesting question, and I suspect the answer for your particular situation will only be revealed through listening. Manufacturers of 3-channel amps that have a shared power supply (one transformer and set of filter caps for all 3 channels) often recommend using the amp to drive the main speakers and center channel. The theory here, as you state, is that the channels needing the power can use it as necessary -- and since the center channel does not (as a rule) need the same power as the main speakers, that makes sense.

From personal experience with my son's HT system, where he uses an Adcom 5503 for the main speakers and center channel, it seems to work fine. To drive the rear surrounds, my son uses an older Adcom 545 amp (100 wpc).

In my own HT / audio system, I currently use a 2-channel Bryston 4B-ST amp for the main, full-range front speakers, and a 3-channel Bryston 5B-ST to drive the center channel and surrounds (all smaller speakers). The 5B-ST differs from your 8008x3 because each of the 3 channels have their own transformers and filter caps.

I think the real issue here is how to make best use of the power available, which depends on your speaker configuration. Do you have 5 full-range speakers, or are the main speakers full-range in combination with smaller, limited frequency center and surround speakers?.

If you have the latter configuration, and your center speaker is reasonably efficient (say, 87-88 db or higher), then your 8008x3 should work fine for the center and surround speakers. This will ensure that the full-range main speakers have the entire power supply of the 8008 (2-channel) available to them.
I basically agree with Scott but would go so far as to say that I would HIGHLY suggest using your highest quality amp ( 8008st) for your mains and the three channel ( 8008X3 ) for your center and surrounds.

Not only does this offer the best stereo seperation due to the dual mono higher current design of the 8008st for two channel use, you would also have what i would consider to be the best foundation for "dynamic power on demand" for the entire system when running in surround.

The reason that i say this is that the rears simply don't get as much action or high intensity volume requirements on HT as the mains or center do. This allows the center to pull harder from the common power supply of the 3 channel amp for the majority of its' usage without really compromising the rears. When most major effects in the rear are taking place, the center channel is typically not under high demand. Kind of a "sympathetic co-existance" if you know what i mean. The mains remain "unflinched" through all of this since they have their own amp, presenting a consistent stereo image regardless of what the other channels do. This should give you the best performance of both worlds ( 2 channel & HT ).

Sounds like you've got the basis for a pretty nice system with plenty of "oomph" : ) Sean
Sean's point offers a good clarification: if you use your system for both audio and HT, and audio is important to you, then -- all other things being equal -- use the highest quality amp to drive the main speakers.