The midi is used to get control between the consoles. You have to use the ADAT and 2 tr digital to get any audio to pass between the units. You can easily get 10 channels of audio (your choice through cascading patches) or if you add the MY16AT cards you can get up to 26 channels between consoles. These channels can be anything you want such as aux sends-main send-solo-subgroups-channels-inserts or whatever. There is huge flexability, but it takes a while to figure it out and how best to actually use it. THe yamaha manual tells you how to do it, if you what questions to ask it.
I am enclosing a manual I wrote for our customers (it is church use based). It is still uneditied (so don't complain!! HAHA) but does give some basic usages that come from the classes I teach on the console. It may give some operational guidence, but does not go into detail as it was sritten for the end user.