Are you trying to say that you want to use prototype as well as jquery in rails project? If you insist then I would like to ask why, because both 'try' to achieve similar results. Why would you like to carry two bazookas to kill a single person... ;)
Still if you insist, they conflict if used together. I would suggest that don't include the javascript libraries in your layout file(application.html.erb) and include them separately in individual pages (depending on your choice for different pages), or controller specific layouts, using some code in application.html.erb, or any other way you deem fit. But to warn you - that is ugly!