How to sync iTunes to iPad
Your first sync will bring items from your iPad to your iTunes library. Once that is done via iBooks on your mac drop the PDF into that app. Then when you sync again that PDF will show up on your iPad. 

Or you can just email (iMessage, AirDrop) the PDF to your iPad and then open it and save it into iBooks. 

If the iPad already has media content then you will want to this - https://discussions.apple.com/thread/4256950?start=0&amp;tstart=0