Do you have it set to sync collections on your Mac and iPad?
From iBooks: How to sync iBooks between devices
Collections, highlights, notes and bookmarks sync across all your devices. Use these settings to synchronize these features:
On your Mac, open the iBooks app and select iBooks > Preferences > General. Then, select the option to "Sync bookmarks, highlights and collections across devices". This setting is on by default.
On your iOS device, open Settings > iBooks. Then, select the options to "Sync Bookmarks" and "Sync Collections".
Using Sync Collections with PDFs in iBooks
If you turned on Sync Collections, iBooks will keep your PDFs (and non–iBooks Store books) in the same collections across all your iOS devices and Mac (if you're using OS X Mavericks). For example, if you have the same PDF on all your devices, when you move that PDF to your Sci-Fi collection in iBooks on your iPhone, that PDF will appear in your Sci-Fi collection the next time you open iBooks on your iPad.
Regarding your response to FreeWizard's question: Does your response come from personal experience on this very subject? or from a general "it should work like this?" The reason for my asking is that I have exactly the same situation as described by FreeWizard, a bunch of PDFs grouped into Collections in iBooks on my Mac (Mavericks all up to date) and on my current version/release iPad, the Sync Bookmarks and Sync Collections options are set to ON, just as you describe; yet the Collections information does not make it to the iPad. I note that FreeWizard did not respond to your suggestion, and I infer from that that your proposal did not work for him/her.
I dont know for certain pdf collection transfer unto apple devices, but do know that certain books are bought through different stores because certain store and regions dont have diverse books etc; therefore it is done through itunes book ipad/iphone book sync section. In regards to pdf files; i believe you should download the pdf file app and then synchronize it via itunes in the bottom; by adding file by file through itunes eith the ipad/iphone connected to the mac unto the pdf app, kind of like the goodreader app. Now when it comes to pdf collections, of that i am not certain.