As long as you know the amount of fuel going into each vehicle, and the cost of it, the averages will wash out correctly anyway. I'd say do NOT select the "Partial fuel up option" -all you need is miles per consumption, not the reletive fullness of your given fuel tank.
How do you fill the vehicles?
Portable gas cans; just count the number of full cans added and estimate the last.
Hand pump; measure the volume dispensed with each pump or crank, then count the cranks.
Powered pump; time how long it takes to fill a known volume, then time the fills.