To use ecutek software to flash car you need to have ecutek cable and the Deskey dongle (it looks like a usb stick but its not) plugged into PC at all times.
Their is no need to reflash tune unless the tune has changed ie yu got a new updated tune.
If you need to reflash use Detect vehicle then program ecu option then query ecu to check connection. then in top left of screen window their is option to select tune file to flash
maybe read here
http://www.ft86club.com/forums/showthread.php?t=117520
Theirs also help files supplied with ecutek that can be accessed via the ecutek menu