This link might help a little with the icons changing color versus the colored circle or square or background changing color:
Also as far as layering is concerned I think you mean nested maps maybe? Checked out nested maps in the admin guide:
The basic idea is:
To create a nested map:
1. Drag a map from the Maps group in the left pane onto the parent map, and then position the map icon appropriately.
2. If you want the status of a child map to also indicate the status of its child objects, complete the following steps:
a. Right-click the child map icon on the map, and then select Properties.
b. Check Include child status on the Status properties page, and then click OK. The object status icon now includes the secondary status indicator.
You can have a map for each campus and have them all linked from your main high level overview map.
With network atlas you just really have to experiment a little. The tool has definitely gotten better with each version. Also it looks like they are going to update the coloring very soon.