Hi.
Thankfully, This looks simple to figure out.

First, yes,
always use a fuse. Put it as close to the power source as possible. Fans do short out, and so do wires.
Also, for the sn95s, they used a separate electronics box (?CCRM?) and the EEC to control fan speed via PWM ("pulses the voltage on/off" the correct way to control DC motor speed).
So, the sn95 fans are a
single speed fan. The variable speed is done by electronics (the correct way to do cooling).
The black wire is ground, the blue wire is power.
A dual fan sn95 setup should be pretty good. Now, we get into the desired use for
your car.
For a
street car, I'd suggest a DCC controller to get better gas mileage and better life from the alternator and battery.
For a
track car, you have a few options.
*I* would suggest that you
always run at least one fan. Putting both fans on a switch means a few grand in melted engine parts sometime in the future. Sorry, we all make mistakes. It's too easy to turn both fans off and end up with melted metal.
So, you could use a relay setup that turns both fans on. Or, in this case, the second fan.
Disclosure: I haven't emailed Brian in 5+ years, or even chatted on the forums. A
long time ago, we did have a few correspondences - via the forums.
I have zero financial interest and gain in the DCC. But, I like Brian, the design, and I personally have a DCC controller (the WP85) that I bought through his website a few years , I never told him about it. I was just one of the regular customers. And, yes, it did take
more than a month to get the unit. No such thing as email updates, etc. Kinda like ordering in a black hole. IMHO, BFD!

I knew that was the case, and for
my money, I greatly prefer the DCC units to anything else out there.
With the above said, I suggest using the:
WP85 $174.95
Fan Control
Yea, it is an overkill for the fans. But,
the hotter the electronics run, the faster/greater the failure rate. So, I want my fan controller to be taking it easy, not being hot, and saying "That's a load - ha, ha, ha".
Ever have an electric fan or controller go on you? I HAVE! IMHO, for the cost of my engine, and security of mind, I want the best cooling I can (within reason of course). So, I also like dual fan setups and using real FORD fan motors.
For cool-down, just wire up a simple switch to the AC input on the DCC controller to run the fans at full-speed.
And, yes, the DCC web-pages and links and instruction leave a lot to be desired in terms of being up to date.
From:
WP60 Install
AC input
If the vehicle has air conditioning and a factory installed electric fan, connect the blue AC input wire of the harness to the unit and to the positive terminal of the OEM fan wiring harness. If the vehicle has air conditioning and originally came with a mechanical fan, connect the blue AC input wire of the harness to the air conditioning compressor input.
Testing the unit
Start the car. If equipped with air conditioning,
turn on the AC, the fan should run at 100%.
Or, as I mentioned before,
1) Run the first fan always -
through a separate relay that gets activated when the car turns on.
and
2) Run the second fan though a driver-controlled switched relay.
My concern with that type of setup is that there is still a chance of making a human mistake (like we
all make), and not having the second fan running and the engine gets hot for some amount of time before the temperature gauge is checked and noticed. If the engine gets too hot, it'll cost more for a head gasket replacement (gaskets, anti-freeze, oil, etc) than for the DCC controller. Also, how much does it cost to do even just a few runs on one day?
I say first put the money where it makes the most sense and gains the most.

My full-time gig my be with an FFRDC (part cost is often secondary when you're building only a few), but I still have my part-time, very cost sensitive & high volume, commercial product gig. I love telling people at my FFRDC how at my commercial gig, I had to spend 3-5 days to convince and prove to management to add a
25-cent FLASH chip to the design.

So, figure that at my commercial gig, they spent about $2K in engineering time (they pay me per hour) to decide if we should ad a 25-cent chip. With the yearly volumes for that product, that made sense (and cents). But, if we where building only a few, then spending over $2K discussing the sense of adding a 25-cent chip would be foolish.
So, as I said, *I* consider where it makes the most sense to put the money to get the most back.
And, in my view, for a Fox or sn95 5.0, they need as much help in the cooling department as possible. The 5.0 throws off a ton of heat (it's very inefficient). And, the engine bay is tight with poor air flow.
Good Luck!