Masterchain is a "system-level" chain for stuff that affects the whole network, and workchain is where the "regular life" happens such as users sending each other Toncoins. There is only one workchain at the moment, but there could be possibly much more in the future.
You could probably think of the masterchain as the "basement" of a building and of workchain(s) as the "floor(s)" where people actually live.
So mostly you don't need to deal with the "basement", you just do your stuff using the basic workchain. And if you'll need to "go to the basement" (directly interact with the masterchain) for some reason in the future, that would probably mean you got into some low-level stuff, and by that time you'll know the difference.