Good page:
http://cbio.ensmp.fr/~thocking/primer.html
Shows how to use .Rprofile and .emacs file. This is the old fashioned way,
(setq inferior-R-program-name "/path/to/R");;
I need to return and get this right, once and for all. So I started this page as a reminder to self. Google for ".emacs file ess-directory-containing-R". that is the way to set it now.