Peter there are several ways to wire this all up. Yes the temperature controller can switch (at least mine can switch up to 10A), however it is just a switch it cannot regulate - so its either on or off as per its setup. The PWM is commonly used for motor control functions so running slow or fast - so to speak, is its forte. More info here:
http://en.wikipedia.org/wiki/Pulse-width_modulation
In theory you could run your PWM through the controller relay contacts and be able to regulate when it is switched on.
Do you even need a PWM, not if you want the TEC to be running flat out all the time and drawing a continuos 6amps from your power source - maybe not a concern if your on an AC/DC converter at home. It is useful on battery power in my opinion.
Re the issue of possible differential regulation of the TEC and the fan. I see no real benefit in regulating the fan separately as it only draws 0.18A whereas the TEC needs 6 Amps and produces all the heat. It is also risky to turn the fan off or dial it down if the TEC is receiving full power - its a good way to burn out your TEC - I did that with the first TEC I bought.
I will initially set it up with the TEC powered via the PWM . I will probably run the fan off the same power feed. Initially the temperature controller will be reporting the internal camera temperature only and if it does switch anything it will be a simple Red LED to signal the threshold is crossed. I prefer the initial field testing to be done this way. I want to be able to work out the PWM setting that holds my target temperature over the length of my imaging run (and this may be different on different nights). Remember if you separate the TEC and fan power, the fan needs to work , you might want to dial down the TEC but keep the fan running hard to avoid heat buildup in the heatsink which will pull up the TEC. Rowland can probably control them separately (looking at his circuit). But I can't see any reason to switch off the fan at any time.
Keep in mind the lag time - the time it takes for a shutdown TEC to get back to your target temperature. If you do switch the TEC off then keep the fan running if you intend to restart the TEC. By experimenting you should be able to determine how long it takes for a shutdown TEC to get back into the zone - this will allow you to work out at what temp do you turn it back on. Your controller can handle the switching but leave the fan running.
Finally, reading the controller instructions, it's pretty clear that you can set it so that it will turn off when your target temp is reached and start up again when your 'd' value is reached (ie set 'C' + d = start. At 'C' it turns off again until C +d is reached again). But again, only for the TEC, I would not turn the fan off because of heat build up and its affect on recovery time.
This is just reflects my experience so far and I am by no means an expert on this subject.