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Two options:

1. If you have the standard pre-printed check with check number, MICR line, bank information and company information, you can uncheck the blank stock option on check settings screen to fill in data only.

How to fill in the check data only
https://www.halfpricesof...ware/fill-out-checks.asp 

2. If your pre-printed check is not the standard, you can hide the fields on check layout screen by following this guide.

How to hide one field on check
http://www.halfpricesoft...e_one_field_on_check.asp 

Thank you.
If you have further questions, please contact us directly at services@halfpricesoft.com
Small business payroll & tax software solution
http://www.halfpricesoft.com 
My checks have check numbers on them already. Is this feature able to be turned off?