Yes, you can run a live payroll using the ATF Payroll Option and write checks.  The indivdual checks will not automatically go to any general ledger accounting software package however; you can export payroll totals to the QuickBooks General Journal (A-T-F Payroll Menu>Options>Import & Export Options>S. Export to QuickBooks General Journal).  For other software packages,  you can export transaction data from the ATF using Options>Import & Export Options>F. Export Tab Delimited Transactions w/Employee Data, which will create a Tab Delimited file that you may import into some accounting software.