Please add an additional layer that overlays the element (or group) that can be toggled on and off. No need to address the same element (i.e. default button) each time it is used, once is good. This should also be defined in the design documentation.
As for scrolling effects or other animations outside of hover/rollover effects, a note in the PSD or a separate text file (read me) with details will suffice. Where necessary, we can arrange a quick screen share with a designer to review and discuss as well. It is important to ensure any custom effects will work in the Campus Suite platform.