I am curious why when I use the onboard mic and the shotgun mic (Sony HVR-Z5U) and drag it onto my timeline in premiere pro cs4 it only show one audio track? Is there a setting there i am missing in camera or in Premiere Pro? Or is this the way Premiere handles the audio from two different mics? New to editing so forgive me for the novice question...

Yep, if it's a stereo track then simply Breakout to Mono... (http://help.adobe.com/en_US/PremierePro/4.0/WS1c9bc5c2e465a58a91cf0b1038518aef7-7f42a.html)

Thank you...