The answer is...it varies.

One of mine (my original I/S) was set up with a custom controller I designed. All four were running lights, the outer two were brake and turn signals (though the flashing one would not act as a brake light) and the inner two were also brake lights. Additionally, that bike sported a fender-mounted OEM taillight.
In a savage act of pilfery, my current ('01) I/S lost its trunk to my '99 Tourer. The outside lights were set up as brake lights.
I've another trunk in pieces for my I/S. When it goes together and is mounted I'm not sure what I'll do with the lights. There's a Badlands R-S-T module hooked into the I/S' rear lighting system at present so I'll do a little puzzling with regards to setup. Maybe make the outer two into R-S-T lighting and leave the inners as running.