...
Select "Create new project from JTAG chain" and press "OK"
Select Port: FTUSB-1
After scan 2 MachXO2 devices should be detected in chain
In first column click to "File Name" and then to "...". Select "SCM_REV*.jed" file (Master CPLD File).
In second column click to "File Name" and then to "...". Select "SCS_REV06*.jed" file (SlaveCPLD File).
Run "Design"->"Program" from main menu
Wait operations to complete