Can you send me a schematic?
Considering the relative price of the BB I would be very weary about sinking our sourcing anything over 20mA. I couldn’t tell from your description, but if you’re driving more than one led, you need a transistor to act as a buffer between the BB and the leds. As for the polarity option, it is almost certainly referring to whether or not the duty cycle is inverted. Pwm waveforms usually start the period high, then transition to low at some point for the rest of the period. Changing the polarity would reverse this. And as for your comment about current direction, if the pin is configured as an output, it will allow current in either direction depending on what you have hooked to the output.
Please post a schematic on the mailing list before you fire it up!
-JonRW