you should always save work work as an.xcf file so that you can go back to it if you like. that format preserves the layers.
.jpg is ok for things that don't have lots of detail. never keep opening and saving a .jpg as it is lossy. meaning each time you save, it looses quality. note: opening and closing is not saving.
.png is what i always use. it isn't lossy and retains transparent areas.