Here's how to apply Teflon tape correctly: 
Face the threaded male end of the fitting towards you and wrap the teflon tape in a clockwise direction. Start wrapping from the bottom and work your way up the threads (see below). Cover at least half the width of the tape each time you wrap it around the fitting. Continue wrapping until you reach the end of the pipe.

Teflon tape can be used just about anywhere where you have threads. Avoid using teflon tape with compression fittings, hoses, or applications that have an o-ring or gasket.

PROTIP: Try to leave the first thread at the end of the pipe exposed as it is easier to attach the fittings.