Some ways to customize cperl mode

Don't put "else" on the same line as }

cperl-mode's usual automatic indenting (as in "indent-region") changes

}
else {

into

} else {

To stop this, use

 (setq cperl-merge-trailing-else nil)

Don't highlight trailing whitespace

cperl-mode's default is to add underlines to trailing whitespace (spaces or tabs at the end of lines). Turn off underlines for trailign whitespace EmacsWiki

(setq cperl-invalid-face nil)
(setq cperl-invalid-face (quote off))

Web links

Perl Monks indent like "Perl Best Practices"