If you want to keep PDF books in a cloud service and only download them when needed you'll have to use a different app than iBooks.
Both GoodReader and PDF Expert have DropBox integration built in. Once you set them up you can upload/download files directly to DropBox.
You could also use the free Adobe Reader app along side the DropBox app. You would use the DropBox app to download and then use Open In to copy it to Adobe Reader.
There are lots of other PDF readers out there.
Basically, you download the books from DropBox to the reader of choice, read them, then delete them when you were done.
iBooks does not have DropBox support, though you could use it like Adobe Reader by downloading in the DropBox app then Open In the iBooks app; delete when done.
While there is no way to copy/sync a PDF directly from iBooks on the iPad to the computer, you can email it to yourself. This is the only way to get a PDF out of iBooks. They can not be synced back to iTunes. Only books purchased in the iBooks store will transfer from the iPad back to iTunes on a computer.
Personally, I do none of these.
Instead I add all my PDF books to iTunes on the computer first, then I sync them back to the iPad. That way I have a copy on the computer, and I can add or delete them from the iPad by changing my sync settings and re-syncing. Unlike syncing form the iPad to the computer, this direction works fine.
However, some people don't like to use iTunes. In that case the earlier suggestions should work fine.