I have some PDF "templates" I markup using iAnnotate. The templates are not necessarily confidential but the markups definitely are. I have the templates in a BoxCryptor folder and, using in iPad, I hold down on a filename, get it to download and then select the "Open In..." option to open in iAnnotate. After I've finished with markup, I choose the iAnnotate share option and pick the "Open in BoxCryptor" option. Then I can navigate to the original BoxCryptor folder and choose to upload and save the final PDF there. BoxCryptor usually indicates the file already exists and asks if I want to overwrite. There are times when it just appends a numeric digit to make a unique file name and uploads without asking - I haven't experimented to determine which case causes which. However, this works but it's not a clean as a native BoxCryptor interface in iAnnotate. I just wonder if others have found a way to use the two in a more simple fashion.