Get a free online storage account (box.net, dropbox, sugarsync, google drive or whichever of the dozens of free offerings you like - I use box.net most of the time and it works well). Then, put your PDF files up on the cloud storage account and only download the one or ones you need at any given time. You can limit your transfers to only when you have a free wifi hotspot available. That will minimize how much space you need to use for PDF document storage.
As others mentioned, you have to load a PDF into an app to even see it - iBook if you like, or any of the dozens of PDF reader and editing apps available in the app store (Adobe Reader is available there, and is free).