If you have Apple's iBooks app installed on your iPad you can use that to save PDFs to read offline (if you don't have it already then it can be installed from the app store).
If you then tap on an open PDF you should see two options appear at the top of the page: 'Open in...' and 'Open in "iBooks"'. The second option may change depending on which other apps you have installed, so if that doesn't say iBooks select the first 'Open in...' option and that should give you the option to 'Open in iBooks'.
You will then be taken to the iBooks app where a copy of the PDF will be saved and can be accessed even when offline.
If you have any problems following these steps please get in touch.