You'll find the partial fuel-up option on the Add a fuel-up form just above the Fuel-up! button. This will tell Fuelly you didn't fill your tank all the way and it'll be reflected in your stats. Here's a little more info about partial fuel-ups.

We've found a big cause of wildly inaccurate mileages is partial fuel-ups. The system was assuming each fuel-up was filled completely each time. You can also go back through any old fuel-ups that were partial, click edit, check the partial box, and save. That should even out any problems the partial tanks were causing.

Please post here if you have any trouble with partial fuel-ups.