I think I'll answer your questions in reverse order:
* I like to think of modeling as connected to a domain, that which you are modeling, but yes. If you have a set of legacy tables that are in reasonably good shape and describe the domain, then relations become ties, tables become anchors, and columns become attributes. If there are reference/lookup tables they also typically become knots.
* The dot means that the graphical symbol is pinned down and will not be moved around by the automatic layout algorithm. Click again to release or select "Release all" from the Layout menu.
* The name (text) is red when not all required information has been entered in the Edit pop-up menu, or when the information entered does not follow our naming conventions.
* Ties cannot have attributes. Natural keys of ties are therefore typically found by inspecting attributes of the adjoined anchors.
I also recommend watching our video tutorials on this page:
http://www.anchormodeling.com/?page_id=186