Many contractors elect to keep their prevailing wage work payroll separate from the private work payroll.  This is completely acceptable provided that both amounts are reported on the CPR in the given workweek.  The two illustrations below show how this may be accomplished.  The first one simply has both checks' separate amounts in each of the categories as well as the two check numbers.  The second has two check numbers yet the amounts have been combined for a single entry into each category.  Provided both check numbers are listed, this practice is acceptable as it does represent factual details.

A word of caution about utilizing the "separate check" system:

Employers are required by law to deduct and deposit the employee's personal income taxes at the rate precisely consistent with the Form W-4 (Withholdings Exemption Certificate) submitted by the employee. The standardized tax tables are predicated on the amount and frequency of payroll on an annualized tax-year basis. Since these tables do not include rates for separate check "parallel" payroll schemes when two or more smaller gross pay amounts are created on separate checks the aggregate deducted amounts are proportionally lower than if these gross pay amounts were combined for a larger annualized gross income tax rate.

Additional tax withholding may need to be calculated in order to satisfy the employer burden of deducting and depositing the employee's pay-as-you-go taxes!