Since you will have a separate CD player I don't think that it would matter, the sound quality then would mostly depend on how you encoded your mp3/WMAs.
The bottom line is that for audio you want a card that can output at a sample rate of 44.1Hz IF you don't want to lose some sound quality due to the resampling. But honestly it doesn't make much of a difference to me (except for DVDAs and Super CDs). I already have most of my CDs ripped in my PC and they sound good enough to me! I'm sure some people might disagree and I hope they'll chime in.
It's really up to you; how do MP3 rips of your music sound to you?
Bottom line if you will use this rig for movies and ripped CDs then I think you would be fine with whatever you chose (onboard sound w/ SPDIF, sound card).
