for an overview of the MySQLi server behaviors, see the MySql Server Behaviors series of tutorial:
http://www.webassist.com/tutorials/MySQLi-Server-Behaviors-series
there is a video demonstrating the use of the Data Modeler and Query Builder
In the advanced Query Builder, there is an option to use distinct. The referenced video and tutorial should answer other questions.
I have not use the ADDT tools, nor do i have access to the manuals.