You're over complicating things. For each cheque deductions are calculated on the total gross earnings, and the assumption for ease of payroll calculators is that the gross amount is what you make every paycheck. For example, if you have huge OT one pay period and gross, let's say, $4k, tax and deductions are calculated on the assumption you make $104,000 ($4k x 26 periods if bi-weekly).
That's why bonus cheques are usually taxed to hell.
But at the end of the year it all goes by your actual gross earnings, so if you were over taxed on some cheques it will all work out in the end.
Use this calculator:
Payroll Deductions Online Calculator (PDOC) - Disclaimer