There are plugins available to make the ATI Remote Wonder to work under MCE, but I personally like the MCE remote better than the ATI.
I use an universal remote (MX-500) for everything else, but for MCE I still prefer to use the Philips MCE remote.
However, after reading the recent Harmony remote thread here, I have decided to give the Harmony 680 a try ... including for my MCE needs. I will report back in a couple weeks on my experience.
If you DO try out two MCE cards, please do let us know about your experience.
Also, if you tell us a little bit more about what exactly is causing you stress in getting your HDTV on HTPC working, there are many of us here that will be willing to help.
Start by posting a detailed configuration of your machine (hardware and software), how far you have progressed, where you eventually want to go and last, but not the least, what is blocking you right now.
For some issues, like multiple HDTV tuners, you may not get a ready made answer since few people here would have actually tried it ... so in those cases you may have to lead the way, try it out and let us know.
If I get any convincing leads that two ATI HDTV Wonder cards do indeed work well in MCE, I will likely get another ATI card. if I do so, I will be sure to post my experience here ... I will need to do some research first, so it might take a while.