One of mine is number 4000 something at Diskuspublishing and another has been waiting 22 months for a decision at Hard Shell. Probably the most important difference is the contracts themselves. With most independent e-publishers, you only 'lease' them electronic rights for one year, renewable by mutual consent. You keep all your other rights, such as audio, hardcover, paperback, movie, etc. Then, there's royalties.
E-publishing standard is to get a statement every quarter instead of twice a year.
Again, this may vary a bit from publisher to publisher. In that case, the company usually splits the 'net' price that they get from the bookstore with you. Hard Shell sent my galleys by snail mail. The other two did theirs by e-mail. Just like in print publishing, unless you're a big name, you have to do some of your own self-promotion.