The way the two protocols operate is different.
http://citeseerx.ist.psu.edu/viewdoc...=rep1&type=pdf
should give you an idea of how eDonkey works. There is no shortage of information on bittorrent
I can't say much in terms of which is better.
eDonkey is much older than bittorrent, so ED2K servers tend to have more and perhaps rarer files available. However, thousands of files are spoofed on eDonkey servers, most files are pornographic, and dowload times tend to be slow even without firewalled connections. YMMV
