Bookends has built-in pdf annotation. If you prefer another app for this purpose, Bookends lets you export pdfs to other apps, where they can be read and marked up, then exported back to Bookends. This example uses iAnnotate, but a similar workflow would be used with other pdf markup apps, such as PDF Expert and GoodReader.
To open a PDF from Bookends in iAnnotate, do this:
1. Open the PDF in Bookends and tap the Forward button in the upper right.
2. Choose iAnnotate.
3. Mark up the pdf (take notes, etc.).
4. Send the annotated pdf back to Bookends. In iAnnotate, you tap the tab containing the document.
5. Tap Share, then Open In.
6. Select Bookends. Bookends will usually guess the right reference to attach to if the file name is the same. If it is not, you can select the reference yourself.