The mII and sp13000 did allow for native 800x480 output, so you could just set the xserver to that resolution.
AFAIK the en15000 doesn't have any linux drivers (or stable windows drivers) for a lot of its hardware, so only generic drivers will be able to be used.
To get the most out of the hardware that you can I suggest using EpiOS (I have no experience with it) or gentoo (which I use) as they are/can be built specifically for the Via hardware.
P.S. Nice specs for the machine, let us know how it turns out. I need to upgrade my original Epia 800 with 256 ram