Hi,
When a conflict between JQuery and Mootools occurs, it's usually because the jQuery library ovewrites the javascript variables used by mootools. By installing and configuring that plugin, it avoids that jQuery overwrites these variables and thus avoids the error.
You should not disable jQuery. If it's there, it means that it is used by something on your pages.
And yes, the problem with the menu is coming from the same conflict. Fix the Mootools/jQuery conflict with jQuery Easy, and that will also fix the menu.