There is no SDK or embeddable component available or planned at this time. What you can do, and we have many integrators going that way, is to run PDF Annotator from within your application on the command line.
Depending on your requirements, there are a couple of undocumented features to customize and restrict the UI, and you can wait for the process, or set a copy hook on the file you opened, to get notified once it is written. Also, we offer customization, depending on what exactly you would need. Please contact us for details if this would be an option for you.