Will you receive full power from your amp by going through a 5.1 sound card or will your amp be somewhat limited... somehow... just curious.
What do you mean? You mean if you run the sound from the sound card to the amp right? It shouldn't be a problem. Some people talk about losing power by splitting the signal when running the sound card in regular stereo mode to a 4 channel amp.
If you want full 5.1 sound though you'll probably need two amps (one for the front/back speakers and one for the sub). If you don't have a center channel you can lose the sound for voices when watching a movie, but this isn't a function of the amp.
Since you're car isn't a theater, many have said to avoid the 5.1 all together. When running in 5.1 mode (for the Epia board at least) you can't use the line in so you'll not be able to use a non-USB tuner card if you want that as part of your system.
You will not lose center channel if you don't have center speaker. all cards come with software that allows you to use 4.1 or 5.1 speaker setup. No, you will not lose power by feeding the AMP off the card, just make sure that your AMP has line-level input. The car HU has speaker-level out. If you want to use both, then you will need to convert the speaker-level out off the HU into line-level and then use an A/B switch for source select (Carpc or HU - you CAN'T use both at the same time, you will kill one of them if not both).