PocketBib does not currently support annotation, but you can export PDFs for annotation in another program (like GoodReader or iAnnotate), and then re-import them back into PocketBib. PocketBib will then offer to upload the new document to Dropbox, replacing the original.
First tap the action menu at the top of the PDF viewer, then tap “Open In...”:
Then select your preferred annotation app and make your annotations.
When you’re done, send the PDF back to PocketBib using the “Open In…” menu in your annotation app. Once you’ve sent it back to PocketBib, you will then be asked to upload the new file to Dropbox, replacing the original.
If you saved the annotated PDF as a “flattened PDF”, you will be able to view your annotations in PocketBib. If you didn’t flatten the annotations, they can still be viewed in other applications that support “unflattened” annotations.