You should wrap your jQuery code into a jquery safe block:
(function ($,undefined) {// ... your jQuery related code here })(jQuery)
This ensures that everything jQuery related and soped to $ uses jQuery overriding Prototype's $ function. As long as you have no plugins that aren't noconflict aware (ie. use this same approach which is pretty standard) this should work to keep Prototype and jQuery separate. Just make sure you use non-obtrusive JavaScript for all your JS code and you'll have no problems.
You can also use jQuery.noConflict:
http://learn.jquery.com/using-jquery-core/avoid-conflicts-other-libraries/
but frankly that's more limited although that might be a good way to make clear what's jQuery and Prototype.
+++ Rick ---