I'm not really sure actually, I just stripped all of the excess .css out and left main.css, but I write alot of my own CSS so it's not a big deal for me.
This is just a guess, but I think the altskin.css is if you install a different skin other than the defualt x-cart skin.
haven't really looked into it too much. If you have a altskin.css I believe you alter that one since it is called later in the html and will have precedence over main.css.
If you encounter a tag that is not in altskin.css then look in main.
Hope I didn't confuse you more.
Ash