I hope you get this solved, because that is very similar to the setup I will be working on (once I get my new PC back - power supply or motherboard fired within 24 hours!) I'm planning to run both my 24" monitor and my 46" TV off DVI ports, with audio supplied through the DVI port via a DVI to HDMI adapter and internal SPIDF connection from the motherboard to the video card. This may work with my current DVI to HDMI cable, but I doubt it.
Currently I'm running my monitor off VGA (through a KVM switch) and the TV through a DVI to HDMI cable (cheap from monoprice.com). I'm going to try upgrading the KVM to a DVI version, since I use my 24" monitor for work and play with a wireless keyboard and mouse (try making THAT work through a KVM switch!)
I don't run my TV in clone mode, so I'm not sure if that would be a problem with my setup, and I don't run video off the motherboard. In any case, my new PC will be totally different, and has the capability to run 2 (or 3) video cards in SLI mode.
OK, geek mode off. I don't really know half of what I am talking about. I just read the web and find somebody that has already worked out the bugs and do the same!
Good luck to both of us.