Is there a software equalizer out there that lets you equalize a channel at a time? So if I only want to change my center speaker, my other speakers stay normal.
You can try using the built-in SB software. It should have some volume control on a per-channel basis. However, you won't be able to actually equalize it (ie: change the 2khz volume for the center channel).
The center channel isn't supposed to be putting out any bass. It's mostly meant for vocals (in music and in movies). The bass is supposed to be picked up by the side channels and the sub, not the center channel.