There is nothing wrong with doing a full fill-up off a partially used tank of gas, it can still yield accurate MPG numbers. The most important thing is to do the same thing at the gas station every time ("until the pump "clicks"").
But I will say doing full fill-ups off partial tanks will yield lower MPG give the same constants as you're driving around with more weight (gas) more often.
Conversely driving until you are on "E" and only filling your tank half way will yield better MPG, since you are carrying less weight (gas) around, but you have no accurate way to measure this other than a real time MPG meter such as
http://www.plxkiwi.com/
GL!