how do i match my ibooks with icloud?

What do you mean by "match iBooks"? What is it you are trying to do?

I don't believe that's possible. If you uploaded pdfs to iCloud using a Mac, it's just for sharing with other Macs. As far as I know, you still have to sync your pdfs to your devices as iBooks using iTunes (see http://support.apple.com/kb/HT4227).