There really isn't an accurate way to calculate average fuel mileage without filling the tank full, and total miles on that tank. If I want to calculate my mileage, I fill up from empty, it doesn't matter if it's $30, or $150, I will budget for it if money is a object. If you can't fill up full from empty, you can't track your mileage. Also, many cars have variance in speedometers, and in cars with mpg readouts, can cause a variance with that as well. Same with gas pumps auto shut off.
Although it's not advantageous for fuelly tracking, this is still valuable for tracking overall mileage - top off your tank once and do not* reset your odometer on subsequent trips/fuel-ups. If you continue to track your mileage and fuel added until your next top-up (even if it's a year later), you will be able to calculate your overall mpg/mpl. I just purchased an MPGuino for my vehicle (pre-'96) because it will allow me to track instantaneous miles per gallon and average miles per gallon and the ScanGauge will also do the same for newer vehicles. Again, topping up once or twice in a long time won't really allow you to utilize fuelly.com but will allow you to see what average mileage you are getting overall. Or you could just install an MPGuino or ScanGauge. (disclaimer: I do not sell/work for MPGuino or ScanGauge but I do really like the tracking/capabilities which the tools offer.. hopefully the one I ordered works well).
You don't have to empty your tank to get a full fuel up, only ensure that the tank preceeding it and the current tank are topped off at the filling station. That is a full tank, regardless of how low the tank was prior to the current fill up.
With in tank electric fuel pumps letting your fuel level get too low can cause problems, fuel pumps in the tank rely to some extent on fuel in the tank for cooling, when the pump is exposed it won't cool as well due to air / fuel vapors being much less efficient at cooling the parts than liquid fuel is. Also, the lower the fuel level increases the percentage of dirt, grime, and impurities in your fuel which can lead to both fuel pump wear and clogged fuel filters, especially when you get really low and the fuel starts to stir up the sludge as is sloshes over the bottom of the tank that is uncovered during hard accelerations, braking, and sharp turns, now you're picking up stuff that can lead to a near instantaneous fuel pump failure or filter clog that will leave you dead on the road.
Just my $0.02, but I try to never let my tank get down to the fuel light coming on with 2 gallons left in the tank.