In boxes 18 and 19 of my W2, the local wages and local income tax boxes, it has two different numbers, one on top and one on bottom, which one do I enter when I file?

Put both.

Enter the first in the box(es) provided.  Then click + Add another row for your next one.

I added another row but it says that my state will not accept this return untill the duplicated School District withholding is corrected.

You should contact your employer or its payroll agency to clarify what information you need to report.