As Draigflag says, fill up now, reset the trip counter if you want - enter the details into Fuelly, this becomes your starting point.
Next time you fill up - enter the details and Fuelly will be able to calculate your MPG.
You don't have to have an empty tank to fill up, but you do need to fill the tank each time, don't put half a tank in as this will give you inaccurate figures for the half filled tank (very high MPG) and the next full tank (very low MPG). It won't mess with your overall average, but it's best not to do it that way.
Oh, and welcome to Fuelly.
Oliver
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