It's a design that predates ED, going back to the old FE2/FFE games: two fuel tanks, the "main tank" that powered the hyperdrive and the "reserve tank" that powered in-system travel. In FE2, you had to transfer the fuel from Main to Reserve manually (until and unless you purchased the module that did it automatically for you).
Of course, in FE2/FFE, the "main tank" was just part of general cargo space. You could use general cargo space to store fuel, or cargo, or whatever else you wished. You had to remember to constantly carry fuel around in your cargo space, otherwise you ain't jumping anywhere.
Every ship in ED comes with that auto-refueller module built-in as standard, so keeping the two fuels separate is kind of redundant now. Especially now that hyperjumps can use any fraction or multiple of 1 tonne fuel units (FE2 hyperdrives used discrete amounts - if your destination was 3.5 tonnes of hydrogen away, you still burned 4 tonnes of hydrogen to get there - the "leftover" half a tonne was simply thrown away).
Calling that second tank the "reserve tank" was somewhat misleading; it sounds like a "reserve tank" would be something useful in an emergency when you run out of fuel in the main tank, but this isn't the case. I'm sure I recall it was originally still called the "reserve tank" when ED first came out, but I notice the most recent edition of the manual (which only covers up to version 2.4) calls it the "active reservoir" instead, which is a much more useful name for what it actually does - power the ship's active systems. But the "active reservoir" still only holds a maximum of 1 tonne of fuel at any one time; when it gets empty, it automatically subtracts 1 tonne from the main tank.