Hi zejjez,
You're right - iBooks sync (via iTunes) works only one way, from Mac to iPad/iPhone. If you create a pdf on the iPad/iPhone, there are two ways to get it back to the Mac.
First is to go into iTunes, make sure the iPad/iPhone is connected to the Mac either by WiFi or USB cable, and select it. Then in iTunes go File->Devices->Transfer Purchases from "<iPad/iPhone name>".
Second is to use Documents to Go on the iPad/iPhone and Documents to Go Desktop on the Mac. Put the new pdf in the desktop folder on Docs to Go on the iPad/iPhone and then sync with the Mac desktop, The new pdf will then appear on the Mac.
But I've discovered that with either of these methods, if you delete a pdf from the iPad/iPhone, and then Transfer Purchases or sync with Docs to Go, the file will still be there on the Mac. This is a mess, and I do hope Apple get it sorted out soon. From the fact that Preview has a subfolder in the Mobile Documents folder, and iBooks hasn't, I'm guessing that the intention is eventually to make Preview into a proper iCloud app and make it available in iOS (and, I hope, on icloud.com so one can get at them from a non-Apple platform, just as one can with Pages and Numbers documents). But that is just a guess.