I feel like you should reach out to Payworks and see if they are able to meet your needs. I have really enjoyed working with/in the Payworks system since 2009.
In switching my current company from Ceridian PowerPay to Payworks I was able to save 50% on fees and it gave us way more in flexibility and functionality system wise. Let me know if you need a sales contact to set up a demo and I can pass along a contact.