Forgive me if I'm wrong, haven't played with the stock board for too long (and the manual will explain this, too - you can just take this as an example because I know the general theory is correct) - but say if you wanted to change your rate of fire:
Flip the #2 dip switch on the board to the programming position.
Turn the marker on - it'll cycle through the colours and then settle on a single colour.
Pull the trigger once and it'll change colour, representing then you're on a different setting.
Pull and hold the trigger for a second, and it'll flash (example
15 times to represent it's on 15bps, and then go blank.
You can leave it, and it'll go back into letting you chose what you want to change again, this takes about 5 seconds - or pull the trigger 20 times (again, example
for 20bps, the board will confirm this.
Then just change whatever other settings, when you're done, flip the #2 switch down (the marker won't turn off otherwise) and you'll be live!