For each Category, you can choose if you generally want to "Send a Thank you letter" for that category or not. For example, for the Donation category, you would choose to Send a letter, but for the Tuition category you may choose not to. This makes the data entry faster in that you don't have to uncheck the TY Letter/Receipt check box each time.
Click Tools > Category Manager and click a Category then click Modify. Check or Uncheck the "Send Thank-you Letter" check box.
If you are using the organization feature, you can also choose a default Organization for a specific category. This makes using multiple organizations easier and you're less likely to forget to assign an Organization to a payment. All you need to do is choose a category and the organization gets entered automatically.