Here are the four steps bring a downloaded PDF into iBooks so it will always be available.

1. After the PDF has been downloaded, click the ‘send’ icon in the lower left corner.
   
2. Select the ‘Open in iBooks’ icon (you made need to scroll right to see the icon).
   
3. After the PDF opens in iBooks click the ‘send’ icon in the top left.
   
4. Select the ‘Copy to iBooks’ icon and you are finished.
   

The PDF will now be permanently available to you on iBooks across all your owned devices (iPhone, iPad, etc.).  Enjoy your new iBook!