Their shows are different in how they are judged. MCBA puts all animals up against each other, standards and every mutation. I believe ECBC judges standards completely separate, almost their own show within a show, and everything else is considered a mutation. Their grading system is also different from MCBAs.
Both organizations have similar rules when you join and originally it seemed that MCBA was the eastern half of the US and Empress the western, but now they are really starting to overlap with both groups expanding their territory quite a bit.
ECBC's fees used to be quite a bit higher than MCBA's, but that has changed somewhat.