I can answer you for DM questions.
SQL Developer forum is separate from DM forum
1. While I have been able to successfully import, create new tables and relationships in a relational model I have not been able to figure out how create triggers (Example cascading deletion triggers, APPL_UPDATE_DT triggers, or triggers to call event based functions). Sequences are no issue.
Triggers are created in the physical model. Expand 'Physical Models'->DB->Tables->Table node and you'll see it. Right click to add new.
2. Also I can see the script generates permissions for users for tables that I import from an existing database, but I cannot figure out where to see these values in the tool (to edit them or to add them for new tables I am adding).
User permissions are also in the physical model. In user(and role) properties dialog there is 'Permissions' button.
Also objects have 'Permissions' buttons in their properties dialogs.
3. Is there any more in depth documentation on the tool. I am not looking for how to write DDL as I can already do this manually, but how to use the tool better?
You can browse DM documentation page at http://www.oracle.com/technetwork/developer-tools/datamodeler/documentation/index.html.
Also there are demos at DM main page http://www.oracle.com/technetwork/developer-tools/datamodeler/overview/index.html
Online demos SQL Developer Data Modeler Demonstrations
There was some other links, posted in the forum but I can't find them now. I'll post them here again later or maybe somebody else will