HS uses regions to define where jump gates are triggered, where you can end up with FTL's, where you can use FTL's, where ammo depots are, where the safety warp thingy sends you, where the TW areas are, where flag rooms are, ... all that crap. You can probably guess the function of most regions by checking their names, properties and where they are placed in the current map. Also check the map attributes (eLVL attributes), in HS they use these to define which regions are compatible with each FTL.