First of all, it must be made clear that Mootools and jQuery can work together flawlesly. Mootools is prototype-base but jQuery is not, so they can work on the same page without any issues.
According to the jQuery documentation (http://docs.jquery.com/)
The jQuery library, and virtually all of its plugins are constrained within the jQuery namespace. As a general rule, "global" objects are stored inside the jQuery namespace as well, so you shouldn't get a clash between jQuery and any other library (like Prototype, MooTools, or YUI)..
jQuery no-coflict mode
Although jQuery uses "$" as a shortcut for "jQuery" you can override that by calling jQuery.noConflict() at any point after jQuery and the Mootools library have both loaded.