I just found it, and I thought others may want to know about it. Let's say that you want to change the Minimum Pagerank for ten of your tier 2 projects from 3 to 1. Instead of changing them one at a time, you can change them all at once. From the main screen, select multiple projects using the shift or control keys and your mouse.
After you select multiple projects, right click on a selected project, and then select:
Modify Project=>Edit Only Engines/Options.
Now you can make changes to all of the selected projects at the same time. Great for changing settings like Pagerank, submissions per day, adding and removing engines, etc.