The software uses a filled fuel tank as a reference point for calculating your fuel economy. You use the Filled/Not Filled option to indicate whether you completely filled your tank after a fill-up.
Note that you can refuel at any time; you don't have to wait until your tank is empty.
Also note that this option does not affect your overall statistics, only the statistics for individual fill-ups. If you do not normally fill your tank you can simply mark every second or fill-up as "Filled" and that will keep your statistics up to date and will give you reasonably accurate per-tank statistics.