Perhaps your answer is less obvious than this, or maybe this is what you need.
Before ripping, you have the option to chose the output folder. Click on the browse button to choose or create an output folder destination. (You should also choose the output format and settings.) Once the files are ripped to this folder, you can clear the ExpressRip window by ejecting the source cd.
I work on a pc with version ExpressRip1.43, which works fabulously for me, although I have no experience with iTunes. Best of luck