This htread had some helpful answers and some not. I appreciate the help so will try to summarize what to do here.
First, to sync to your phone you have to plug in or use wireless itunes syncing.
Remember, your books are in the cloud as a purchase just like a song from Itunes, but your PDF's are just like a word document or other random file. They are on your computer and not the iCloud, that service is for backing up your iphone and making purchases available. If you take a breath and think, it makes sense that your PDF's are not saved in this manner. That being said, if iBooks as an app gave you the option to sync with other devices running the app that might be desireable. Of course, this would take a while to sync and download and then people would complain about the app boggin down to sync all the time!
Second, import all your itunes books into ibooks. You will be prompted to do this when you click on books in itunes now but as a precaution you can also do it from the "File" menu in iBooks by choosing "move books from itunes." This will help if itunes was open at the same itm eas ibooks and updates, etc.
Third, sync your phone with itunes. Although the books are "in" iBooks for viewing on your mac, itunes knows where they are so they will be listed under the sync books option in the iphone sync menu. Either check all or pick the ones you want to sync to your phone. They will be moved.
Fourth, to make this painless set up itunes wi fi syncing, select all books as the syncing option and itunes will upload whatever changes each night when your phone is plugged in.
Fifth, if it is a key doc or you ar ehaving trouble, just go with the share buttong and email yourself. It never hurts to have more than one source to grab your key documents from.
Thanks to thos eon this thread that oferred guidance.