I use an editor (Komodo) which supports external pretty printers for various file types and comes with perltidy already hooked up. I have tuned perltidy to match the way I tend to write Perl code so most of the time I run it it doesn't change a lot, but if I am refactoring code perltidy is invaluable for quickly fixing indentation and wrapping lines nicely.

If you use a configurable editor and let us know what you are using. It may be that someone may be able to help you hook up perltidy to your editor. For Komodo see the 'Formatters' section of the Preferences dialog (Edit|Preferences menu entry).