Bays are the area for ssd, hdd and other devices like fan controller, dvd rom, etc. There are different types, the larger are 5.25" and the smaller are 3.5" (or 2.5" for laptop hdd's or ssd drives). Typically 5.25 are external (for cd/dvd) and external are drive bays open at the front. There are also 3.5" external bays for smart card readers, old floppy drives and that sort of thing. 3.5" internal are for ssd/hard drives meaning you can insert the drives into the bays from inside the case but can't access them from outside of the case.