You don't print anything out when you reconcile with Quicken. Have you ever done a Reconcile within the program? You enter your statement information in, and then you put a check mark next to the items that have cleared.
You can write a check on 1/1/2005 and not have it clear until 12/31/2005, and you won't have any problems balancing your checkbook within Quicken. You wouldn't have problems reconciling with a paper register that way, right? The same goes for Quicken.
Intuit publishes books for every version of Quicken, and they're quite good. You might want to pick one up for the version you have and read it over. Making categories for college semesters isn't going to help you in any way, and it will make using Quicken more difficult and confusing.