Hi user '995039',
Out-of-the-box, there's no way to annotate/markup a document from UCM in AutoVue without going through the UCM interface. Access to the documents in UCM requires user authentication, and this is built into the 'View in AutoVue' link within the UCM interface.
It may be possible to create your own custom applet page that connects the user into UCM and allows them to open/annotate documents from UCM, however I'm not sure how you'd want to design this. For one, in order to launch the AutoVue applet and have it connect to UCM, you need to tell AutoVue to open a file based in UCM. Therefore, you either need to be in the UCM interface, or you need to write your own interface that lists documents from UCM. You'd also need to pass the user's UCM authentication cookie through the custom applet page, unless you want the users to always receive the authentication popup dialog.
Hope this helps as a start.