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Our customers can set up a PTO plan and ezPaycheck will calculate it automatically If their companies calculate PTO by hours,

Since your company have special needs (your employees earn PTO only on the first 40 hours they work in any given week), ezPaycheck cannot set up the limits for each week. I would like to suggest you enter PTO manually. You can leave the data as 0 on employee PTO setup screen. ezPaycheck will track the PTO based on the data you entered and print them on pay stubs.

Many companies prefer to use the manual PTO feature because their is PTO plan is not by hours. (ie: each employee get 20 hours on Jan 1, another 20 hours on July 1.)

If you have further questions, please contact us directly at services@halfpricesoft.com
Small business payroll & tax software solution
http://www.halfpricesoft.com 
We currently have salary, 4 hourly rates, PTO & piece work. It looks to me like ezPaycheck cannot support 6 regular wage options. Is there a work around?