If I use the MarkUp Editor, does it reflect the original in the Job Library?

Yes. MarkUps are public by default since we implemented collaborative markups but you have the option to make it private by checking the box at the bottom of the tool panel next to the save button. You can share your markups by sending them via e-mail through the button located in the MarkUp Editor column as well as filtering your assets by markups and adding them to a Lightbox to share with others, allowing them permission to view public markups.

More about the MarkUp Editor:

Using the MarkUp Editor