If you're at your computer with the 'home' iTunes library for your iPad/iPhone you won't have a problem: Open iTunes, go to File: Add to Library, select on the computer the PDF you want in iBooks [on both iPad and iPhone or either] and it will be added to the device's iBooks library when you next sync.
If you are not at your home iTunes Library, though, that's a problem [if you try to sync your non-home iTunes Library with your device, it'll overwrite what is on your device, so you probably don't want to do that]. But I figured it out and wanted to share the process:
Get Dropbox [or SugarSync/Evernote etc. - some program that allows you to sync between your computers and iDevice, and install and use that [each program gives you several Gigs free space with mobile apps. from iTunes Store]. Put the PDF in the online 'folder' as you would normally, open the app on your mobile device and click on the item and it downloads to your device. Then up in the top right corner of the mobile app [this is true for DB] you see an icon with an arrow, click that and it allows you to open in: iBooks, EasyPDF and other PDF viewers/players on your device. If you select iBooks it will save it in your iBooks PDF library to read later. And you can email or print from iBooks.
This worked perfectly when I found an article online I liked, did a Print to PDF on my computer, put it in the DropBox then opened the DB app on my iPad and clicked on the PDF and it opened and by clicking on the icon, it saved to iBooks and opened in that for reading, emailing or printing.