Make sure you have iBooks installed on your iPad/iPod touch/iPhone.
Open iTunes. Select File > Add to Library…
Navigate to the PDF file(s) you want to add. Select one, more than one or a whole folder. Once they are selected, click Choose
Now select Books from your iTunes Library. You should see the PDF file(s) there.
Right-click on the PDF and select Get info.
Select your iPad or other device from the Devices list in iTunes. Select Books from the tab list at the top.
Make sure your PDF is selected and then click on Sync.