If you have the manual saved on your computer (I'll assume you can do that
) just plug the iPad into the computer, click on it in "Devices" on the left-hand side, then click on Apps. You may have to scroll down a bit to see it, but there should be a box with all the apps that can read files and if you click on iBooks and hit the "Add" button, add the PDF file, and then hit "Apply" or "Sync" and after the sync is done it'll be in iBooks on the iPad.
Another way is to purchase the GoodReader app (an nice PDF/image viewer app), it has a built-in web browser where you can navigate to the PDF and save it. Because I have GoodReader, I don't use iBooks for PDF's.
EDIT - One other possibility - Kind of a kludge, but at the same time kind of cool - Look up "Bring Your Own Procedures" in the ForeFlight manual, and use that to put the manual right into ForeFlight.
After all, ForeFlight doesn't care if that PDF is a plate or a manual... Some people last year used the then-new BYOP functionality to load the Airventure NOTAM into ForeFlight under KOSH. Cool!
Same as any other app - Just tap the Home button. (That's the button on the front of the iPad.)