All the boards I've seen are clearly labelled. Each LDD has five pins - Vin(+) and Vin(-) which connect to your 48v power supply, Vout(+) and Vout(-) which connect to your LED string, and PWM which connects to your Arduino PWM pins.
I don't remember what your specific boards look like, but you should have four terminals that connect to your 48v power supply (two + and two -), the LED outputs (one + and one - for each LDD), and the PWM inputs (one per LDD, and usually one ground that needs to connect to the 48v power supply COM/negative DC terminal).
Your controller just needs to send a 0 signal to that PWM pin.
You would need a relay if you want the fan to be on/off, or I believe that O2 has made little boards that you can put an SCW05C-12 on so that you can control it via PWM.
So after having broken the pins off of several LDD by using pin headers on the boards, I'm switching back to IC sockets. Yes, the LDD will blow if one is accidentally put in upside down, but I'm really careful about that now after the first time I did it