I have a number of PDF files in my iBooks library. I just downloaded Adobe Reader for the iPad. I can't see how I can open those PDF files. The only thing I seem to be able to do with them is to open them from iBooks directly. Doing that does not provide me with the features that Adobe Reader would provide (such as searching for particular text, etc.).
Use iTunes to save the PDF FROM iBooks, and to add them to Adobe Reader.
Connect your iPad to your computer. Bring up iTunes on your computer.
To save a PDF FROM iBooks, click on "Books" in the Library section on the left. Select the PDF you want to save and right-click and choose Show in Finder (Show in Explorer in Windows). Go up one level in your computer hierarchy and you'll see all the "Books" (PDFs and eBooks) in iBooks. You can leave them here if you want to view the PDFs in iBooks in the future, or drag them to the Desktop.
To move the PDF TO Adobe Reader:
Return to iTunes. Click on the iPad on the left in Devices. Click on the Apps tab. Scroll down the the File Sharing section as shown below. Click on Adobe Reader. Click the Add button and select the PDFs you identified in the previous step. They'll be added to Adobe Reader
An alternative work around—if you need to open the PDF without connecting to a computer: From iBooks, open the PDF and from the Action menu (square with arrow, 3rd from left) select Email. Email the PDF to yourself and from Mail you can choose to open the PDF in Adobe Reader. (Yes, it's a bit of silly process.) I have also notices that not all PDF in iBooks have the email option—I'm figuring it's on how they got into iBooks in the first place.