The BoB has a hard-wired interface from one of the discrete outputs (I have a similar board, that's silk-screened "P1 - PWM" - so pin 1 is assigned by hardware design to the PWM circuit. No configuration, no nothing (you could hack the card, of course). There's nothing clever, just assign the same output in LinuxCNC to the hardwired assignment on the board.

Most BoBs are similar.