Once your files have been uploaded to the cloud by your tuner and you are ready to program your vehicle open ECU Connect, plug the interface in and go to “My Car -> Program ECU”. And select the ECU you wish to program. Then choose the Flash File you wish to program if it the first time the EVI has been used on this device the EVI-BT communication test will commence more details are here EVI Communication test
There is a video guide on programming and recovery below
If the test has already been done or after you've completed it you can then select the program ECU and choose your ROM. You should check the vehicle conditions before you start programming, pressing the "PROGRAM" Button to start.
To program the ECU, ECU Connect will prepare the Flash File, erase the stock Calibration Data and program in the tuned Calibration.
Once Programming reaches 100% there is a Key Off then Key On sequence and the DTC’s are cleared.
Once this has completed you can select “my car” and perform the requested logs etc from the tuner.
Hopefully this information helps, if you need further description or are having issues please contact your tuner or firstname.lastname@example.org.