suggest you deposit the check on a actual bank deposit.  With no other checks.

The way you would record in QB.   you would record the individual payments, as of you had more than one check.    Using the same check number for all the recorded payments.

Then in make deposits, you would select all the individual transactions which would total the actual physical check.    that way the record deposit in QB would match the actual total deposit.

option - put a note in the comments explaining what is being done.