I want to gradually migrate from Prototype to JQuery in one of my projects (grails 2.0.4), but when I tried to use both libraries at the same time I got some error messages and the JS functions did not work anymore. Turns out JQuery has a compatibility feature you can turn on:
http://docs.jquery.com/Using_jQuery_with_Other_Libraries
jQuery.noConflict()
On top of that there were issues with the resources plugin, which I circumvented for now by manually loading jQuery where I need it.