i use focus based macros and i set the focus macros to the pip swap keys. that way, when i pip swap, the focus gets set to the character in my main area.

here is a link on how to work with focus based macros:
[Keyclone] step-by-step wow macro setup (level 2.0)

whatever you are using for your pip swap keys, create a macro and associate those same keys with the appropriate macro. if you get it set up right, hitting one key will pip swap and set your new leader. then just target and fire... and if all is set up right, your remaining alts will use the new leader for targeting