Master is the main volume control - i.e. the volume for the power amp section. So you adjust the overall volume with that. If you look at it, you will see the master is labelled at approximate power output levels, with 0W, 40W, 160W etc marked on the dial.
Gain is the preamp volume control - so that allows you to set the input to suit the level coming from yout bass/DI box to prevent the pre being overdriven (unless you want it to be).