The first thing you'll want to do is choose which formalisms (meta-models) start up with AToM3.
By default, AToM3 starts with Entity Relationship V3
UPDATE: AToM3 now starts with Class Diagram V3 by default, along with its associated button generating grammar.
It's very similar to Entity Relationship V3 however, just substitute "Entity" for "Class", and "Relation" for
"Association".
(which lets you generate new formalisms) and the Graph Transformation Toolbar. You can change this in Options, press F1 (or Right-Click, File-Menu, Options).
You can close formalisms by pressing F4 (or Right-Click, File-Menu, Close-Metamodel)
You can open formalisms by pressing F3 (or Right-Click, File-Menu, Open-Metamodel)
You can open RECENT formalisms quickly by pressing F7 (or Right-Click, Open Recent-Metamodel)
A formalism appears to be just a toolbar with buttons, indeed the Graph Transformation Toolbar is nothing but buttons, but others, like Entity Relationship V3, are en entire model making environment specification that controls what can be drawn on the canvas, what it looks like, and what can be modified... Hence why we call them meta-models!
You can open models by pressing Control-O (or Right-Click, File-Menu, Open-Model)
You can open RECENT models by pressing F6 (or Right-Click, Open Recent-Model)
You can save models by pressing Control-S (or Right-Click, File-Menu, Save-Model)
You can save models as (some new path) by pressing Alt-S (or Right-Click, File-Menu, Save as...)
To actually make the model, lets assume you have Entity Relationship V3 formalism open
* To link two entities together (but add intermediate points between them), Control-Left-Click one of them (or Right-Click, Create-Arrow), now Left-Click any empty spot on the canvas to drop intermediate control points, Right-Click to remove the last control point, a final Left-Click on the target Entity ends the process. The two entities could also be just the same entity with a self-arrow.
** To link two entities together (but add intermediate points between them AND not connect with random things that happen to be in the way), Control-Left-Click one of them (or Right-Click, Create-Arrow), press SPACEBAR (the cursor changes), now Left-Click anywhere on the canvas to drop intermediate control points, Right-Click to remove the last control point, press SPACEBAR, a final Left-Click on the target Entity ends the process.