Your statement is misleading. It sounds like you fixed it with using both, jQuery and prototype, but actually you just exchanged the prototype based overlay script with a jQuery based script, so that you just use jQuery. There is a jQuery lightbox
plugin, by the way.
Generally you can say that there is a jQuery plugin for everything you find on the internet. So whenever you find something that’s not jQuery and would cause conflicts, just search for a jQuery plugin using the same terms.