When I place a table in MySQL Workbench model, how do I tell it which of my databases to assign the table to?
The database data is under the Physical Schemata section and is clearly visible when you open the model editor. It has the default name "mydb" which you can edit when you double click on it.
If what you want is to dump your model into a MySQL Server then the Forward Engineer Wizard (in Database -> Forward Engineer from the main menu and also available with CTRL+G) will get you there.
Hope this helps.