You should be able to choose which application you use to view pdf files in the FF menu.
I'm using Iceweasel,so it may differ,here's how i do it after installing xpdf:
Then look down the list of file types,and find portable document format.
Change the default application to xpdf,then click close.
Try opening a pdf file to make sure.
And yes,the 64bit flash and java plugins are available from the Debian repos.