I use jquery alot with prototype and i just assign
jQuery to a new variable after loading prototype and jquery like this
...
$jq=jQuery.noConflict();
then every time i call a jquery function i just use
$jq() instead of jQuery or $ ...
It works with most plugins i've found so far...
definatley with most of jQuery-ui (datepicker, expose etc etc)
Saves headache
Alex