AFAIK you can't. It will always do .mobi (I think that's what Kovid has said).
I think I posted this before, but you could use something like Extension Renamer to change them to .prc in bulk (it does subdirectories to if you tell it too).
http://www.brothersoft.com/extension...oad-41537.html
I know it's still an extra step of sorts, but....