In "the big jets," a flowmeter is installed at each engine, and measures the fuel as it is used.
In fuel injected piston engines the concept is similar. The flowmeter(s) must be installed downstream of the return line. In the presurized system, some fuel is returned to the tank, so that fuel must not be measured by the flowmeter(s). I don't know if there is any installation that has a flowmeter for each cylinder, though it is possible.