Do I have to manually enter check numbers for them to appear on check register?
No, the software will handle check numbers for you. First, in the Check Entry Fields section of Preferences enable #1. Need Check Numbers and #11. Auto Increment Check Numbers, then gp to Payer>Check/MICR and enter the last check number used in the Miscellaneous section on the Last Check # line. When checks are added the program will automatically fill in the check number for you.