You can use more than 2 channels each, and yes there are a variety of ways that things can be connected up. I take it from the picture you have posted that you have already downloaded and installed the Routing Utility. If not then definately get that as it allows you to quickly change settings and can store multiple routing templates that can be switched on the fly. There is a version for PC and for Mac on the support page http://www.eventide.com/AudioDivision/Support/Harmonizers%20and%20Rack%20Products/H8000%20Series.aspx
Have a look at the Routing Utiity manual. On the first page is an example of 8 inputs coming in via AES and then being routed directly to DSP A then back out to DSP B before all 8 channels being finally sent out to AES out ADAT out and Firewire out. That is just one example of many ways to route the ins and outs.
Page 24 of the H8000 User manual explains the routing rules.
Personally I have mine connected via ADAT and use the 8 channels in and out from that, but it can be connected in many other ways. Let us know how you get on.