I realize that there is no documentation for aAC but is there an overview about how the system works once you get it up and running.

I am not a Base Camp user and am not interested in their offering and can't find much there anyway.

So is there a how to that exists anywhere?

Milestone can have multiple task lists (and messages BTW), task list can have multiple task. For instance, milestone Beta launch can have two task lists:

1. Prepare product with following tasks:

- build product using build tool
- package version for Windows
- package version for Mac
- test if whole process is working on Windows
- test if whole process is working on Mac
...

2. Announce beta version with tasks:

- write and post announcement on company blog
- upload packages
- update download page
- update releases page
- update homepage to show the most recent version

Milestone <> Task list relation is optional to give more flexibility to the system.

If the Milestones are "bigger" than TaskLists and Tasks, why aren't they right next to the Project Overview tab. It appears, by the tab order, that Milestones are "below" tasks, since they are to the right in tab order. Just a UI thing.