5.1 speakers with onboard 8.1?
 

I have a 5.1 speaker set but my new machine has onboard sound with 8.1 support. Will the 5.1 speakers work without sound loss if the software (eg COD4) is set to use 5.1? Or will that setting simply not work with 8.1 audio board? I guess my concern is that if I plug in 5 speakers and do not fill out all 8, that some channels might just not get played at all. I'm not really familiar with how these surround systems work so please forgive me my ignorance.

First time I've ever heard of 8.1 but you can hook in whatever you have (5.1 in this case) and configure it to use what you have (the 5.1 in this case)

Even if it was configured to 8.1 and you only had 5.1 installed you wouldn't really notice a different as the extra 3 speakers are commonly used as fill-in's for when sound transitions from one side to the other.