There's no way to use CD's automatically but including them to Macros with other powerful abilities used by MaxDPS.
Trinkets and CD's not on GCD could be bound to some keys not used by program since you can press them any time needed.
GCD abilities should be used with hotkeys ("?" - keys).
What are those additional buttons for? (Question marks)
While MaxDPS Assistant works it monitors for character abilities to get ready and uses them immediately after that. Some time you need to use an ability which is not on program list. But it becomes a real problem because Assistant activates abilities rather faster then you and you always get an active global cooldown disallowing any action.
We involved Addition buttons to solve this conflict. Pressing one of those will make the MaxDPS Assistant to give that button the highest priority and activate it upon next global cooldown time expiration. Then the normal action will be resumed.
Additional buttons queue is supported, i.e. you can press buttons 1, 3 and 2 in a row and the MaxDPS Assistant will press them in a same order waiting for GCD each time.
http://www.en.maxdps.ru/index.php?id=54There's no way to bind smth to mouse button other then binding some keyboard key to it with mouse driver software, then using it in MaxDPS.