Simply connect it on E4-4 as explained here, provided that the signal must come from a circuit supplied at 3.3V (if not, insert a 2/3 voltage divider). Aditionally, execute echo pruecapin_pu > /sys/devices/platform/ocp/ocp:P8_15_pinmux/state or config-pin P8_15 pruecapin_pu.
The BBBlue has four connectors for DC motors (M1 to M4) which are the horizontal segments (bidirectional) of H bridges inside two TB6612FNG drivers, with around 1A capability (supplied through V_BATT on LIPO connector). Possibly this is not enough for a rover, so possibly you can connect them to a L298, but I don’t know what parameters are needed to inform ArduRover that you have DC motors on M1 to M4 requiring PWM signal
Not having enough AUX pins on a Pixhawk1 mounted on a balance bot, I inserted an inverter as TTL glue before the L298. It works.