take a look at these images they give you a good idea of the architecture on the issue:
BES well MDS apps but it shows the way data travels through. You get encryption, and wireless sync of your PIM data and redirection of subfolders to name a few features.
BIS much more simple in the way it works. the BIS server goes and pulls messages on a 15minute timer from POP/IMAP/OWA/Yahoo/Gmail type servers, and then push's them to the Blackberry.