I mean by adding an entry to the .emacs file.
In order to enable PDF mode by default in all *TeX buffers add the following line to your init file:
(with-eval-after-load "tex" (TeX-global-PDF-mode 1))
Note that this is the default in AUCTeX since version 11.88, so if you a have a recent version of the package you don't need it to change this by hand.
with-eval-after-load has been introduced in Emacs 24.4. If you're running older versions of the program you have to use this syntax instead:
(eval-after-load "tex" '(TeX-global-PDF-mode 1))