Fighters burn fuel when they light the burners. On the fuel gauge there will be a different colored section on the fuel readout which indicates about 20% of the ships overall fuel supply. That is the fuel dedicated to afterburning. As you kick in the burners, that 20% indicator will get smaller. Once that is gone, you're alotted fuel for your burners is gone and you're now burning you're ships regular fuel supply.
now, when you're cruising normally, your fuel collection/consumption rate is balanced. Acatually, you take in a little more fuel than you burn in order to make up the difference, so you don't have to land out. But, it takes a while, as you only take in about 10 - 20 pts more fuel than you burn.
The way the scoop system works. Basically, if you fly with scoops full open and hit the autopilot, you're going to take forever and a day to get to where you're going. At 360kps, it'll take you about 12.9 days to travel 375,000,000 km. You don't really want to do that, as some missions in Pioneer will be time sensitive. So....how do you get there faster? Well, you kill some scoop power and sacrifice some fuel. So it works like this. To achieve a velocity of 5,000 kps, and still retain some fuel you pull the scoops back to 1/4 on. (it goes: on, 3/4, 1/2, 1/4, off) Now, you've just gained 1,120% more speed, but only collect 40% fuel, while burning 15% more fuel.
phew, long and complicated, but hopefully it explains how the whole system works. You can play around with the scoops while flying. turning them off gives you full newtonian physics, and any setting in between affects maneuvering and all that. Anyway, enough on that.