The numbers on the C325 are a little better, like the Input sensitivity. It also weighs a tad more, although there's probably not much that's audible in these differences. I own the C320BEE and its a fine amp, IMO, especially for the price.
The MP3 input is just a mini input jack that you would use with a male-to-male cable connected to your MP3 player's headphone jack. There is no additional circuitry to enhance the MP3 sound quality, at least not that I can tell from the website. You could probably achieve the same with a simple mini-jack to RCA cable attached to one of the RCA inputs on the back.
It's funny this thread should pop up. I just recently sold my C352 so I could get the C325BEE. For some reason the 325 sounds more refined and open to my ears. The bass seems tighter and more defined as well. The 325 may not have as much power as the 352 but it's more refined IMO.
Another thing I noticed is the new C525BEE is more and on par with the C542 now that it's using the same op-amps in the analog output stage. The differences are very subtle now.