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Don't forget accrued vacation, special deductions, 401k matching, etc.
You should look into 3rd party When you can pay a company to do payroll for just a few dollars per payee, I doubt designing your own system is worth it.
There is no "simple" payroll management system because payroll is not simple.
I agree with stajer's comments. Plus, I would consider security to be a very high priority for a payroll system. If you haven't dealt with PHP/MySQL security concerns before, a payroll system is *not* the place to learn.