jQuery is today the best js library, prototype is a challenger.The reasons why I think this are beautifully illustrated on the following post. To use jQuery in rails install the following plugin:
ruby script/plugin install http://ennerchi.googlecode.com/svn/trunk/plugins/jrails
Here is a list of existing functions which are available once we replace prototype+scriptacuolous for the jquery. Hopefully, this support will improve once we approach to Rails 3.
If you want to use both libraries, you will keep prototype js files, if you plan to use only jquery you could removed them. I particularly think that seems you have decided to use jquery there is few reasons to keep them.
Also, there are two ways to use jquery, I just found this interesting article which speak about a different way to use jquery, not using jrails but instead in a more unobstrusive way. Interesting point of view.
Kind regards and good weekend