How to create an option in the Print menu with Automator
Solution
Kept playing around after asking and found the right set of actions to add to the workflow to get the result I want. In case anyone has a similar question/requirement in the future, the way to do this is:

Create new Automator flow and select 'print plug-in' - This will add the option to the bottom left button when in the print dialog.
(In Automator) - 'Open finder items' - There is a dropdown there to specify the application you wish to open the newly created PDF to. E.g. Evernote (which I used to test to make sure this flow is working) will create a new note with the output PDF within it.