To the common user, BIOS and CMOS are the same thing. But they actually aren't. BIOS is a set of programs on your motherboard responsible for starting/operating your computer. If I recall correctly, the programs are POST, CMOS, and the bootstrap loader. It's been a while though. CMOS is the part that contains changable settings.
So yeah, unplugging the speaker is the only thing. Seriously though, how annoying can a single beep be when you turn on your computer? The beep should signify "Ahh yes, my computer still works." to you. Does to me anyway. And I just leave my computer on all the time too, so it's not like I ever hear it...