Saving annotations in OnCue LIVE is as simple as hitting "Ctrl+S" to save after you've made your highlights, callouts, underlines or whatever other annotations you need. A new saved annotation with its own ID will be immediately available under the source page in the document tree. For example, if you saved an annotation on ID 47.3, the new annotation ID would be 47.3.1. You can also save your treatment by clicking the "Save Annotation" icon on the toolbar.
Updating an existing annotation can also be done in LIVE. All you need to do is make your changes and hit "Ctrl+U" or click the "Update Annotation" icon on the toolbar. This changes your existing annotation and leaves your numbering the same.
BONUS: This also works on a linked document. You can update an existing annotation while showing the video at the same time. For example you can move a callout so that it doesn't cover the video, hit update and you don't have to review your video again.