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".
and from iBooks: Viewing, syncing, saving, and printing PDFs on iPhone, iPad, and iPod touch
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.
ivan