Cheqbook itself doesn't provide payroll, but that's not as big a problem as it may appear.
Payroll is a difficult task primarily because of the complexity and variety of federal, state and local taxes on employees and employers. Payroll requires the timely and accurate filing of returns and making of payments, an almost herculean task compared to what Cheqbook does for you, so we strongly recommend you select a respected national firm that works in the cloud like Cheqbook does. This third party webpage seems to have a thorough list for you www.thetoptens.com/best-online-payroll-services but you can always search for "Online Payroll Services". As these companies are temporarily holding your payroll funds, larger (like Intuit) is probably safer, but you'll have to weigh your own needs.
How to Integrate with Cheqbook - Simple Method
Once you have a payroll service the process couldn't be simpler. Each pay date (most) services will make two deductions from your bank account: one for the paychecks and the other for the taxes and other withholding. The first time these clear your bank, categorize the paychecks to account "Wages & Payroll" and the taxes to "Payroll Taxes". That's it! The next payroll these transactions will fall into place.
Unfortunately the simple method doesn't work for everyone. You may have garnishments, health insurance co-payments, or other amounts withdrawn from your employees checks. You may also wish to categorize with more detail, breaking down the payroll into departments, or the taxes into types. Whatever the reason you need more detail, you won't be able to automate this process, sorry.
Instead when the paycheck and tax deductions clear your bank, we suggest you teach Cheqbook to categorize both of these as "Uncategorized". Then later, when you have the payroll report, revisit and split these transactions manually into the detail you need. Ask your accountant, if necessary, for assistance with this at first. They should also review your work at the end of the year or more often if necessary.
What's to come?
Cheqbook has absolutely no plans to build our own payroll service. However we are in negotiations to partner with one or more of them. Full integration would allow automatic categorization for the more advanced users - the transactions once submitted would be posted as green circles with all the payroll detail, and turn into green check marks when the transactions cleared the bank.
There is no time frame for this at the moment as there is much for us to research in this area before making a commitment to one or more providers. However, feel free to post your thoughts on which services you like best!