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Pre-printed check forms will usually have a sequence number printed on the form. On the other hand the payroll will generate its own internal check numbers to track employee checks. These 2 numbers will be different. When printing the payroll checks the program will request the first form number that is in the printer. This number will be used to create a cross reference file between the system generated check number and the pre-printed number on the physical check. This way you may search for the check using either number.
In the event that you experience a printer jam then you may reprint the spoiled checks. Then you will provide the starting form number again and the system will create the proper relationship with the new number. In fact the system will maintain the two form numbers (one spoiled number and one good one) in its cross reference file. This way you can trace all the numbers uses whether they were good or spoiled checks.