I don't know anything about that board but I'll throw some observations out. I looked all over the site and didn't see any specs on current capabilities but it looks like the outputs marked for super brite LEDs are just straight 5volt outputs with no current limit resistors, so you'd have to be responsible for looking up the specs on the LEDs you use. If the LEDs are rated for 5volts, you hook them up straight to those 9 super brite terminals and ground (they are always on). If the voltage is more than 5, you can't run them. If the rating is less than 5, you need to see the rated current in the specs for the LED, then calculate a resistor to add in series with the LED:
(5 volt supply - Voltage rating of LED) / LED rated current = resistor to put in series.
THe other 3 LEDs look like they have transistor drivers and series limit resistors, but I can't see the resistor color bands on the board picture on the site so I can't tell what rating of current they would supply. I guess we can assume that the resistors were calculated to handle your typical LED (not super brite maybe) which would run 1.x to 2.x volts at a few mA to 15-20mA of current depending.
So....super brite must go on the constant powered 5volt lines assuming they need more voltage/current than a normal LED, and you have to figure out if you must add protection. Most other common LEDs should run safe on the 3 other outputs but who knows. we don't really have specs for the board.