the blue box is the little blue box (hence the name) that greddy includes with it's 92-95 civic turbo kit to control the fuel curves. it just interrupts some of the sensors so that it all works and runs well. with the greddy kit at 5lbs of boost, which is the default boost, the blue box will run your car comparable to stock in terms of drivability. with the afc hack you might notice a wierd idle and some hesitation when accelerating...but not too noticable. the afc allows you to put bigger injectors on and up the boost, and offers more versatility than the blue box.
i'm using 440cc injectors and a vortec 12:1 fmu, as well as a v-afc.