If you've done it a thousand times, you can easily answer your own question with a few experiments. Go up on some of those old roofs when the fan is running, or go into the attic and force it on first. Then go over to the box vents with some strips of paper and see if they are being sucked into the vent. If so, close off the vent from inside the attic and you're done.
You want the full air flow of the fan to draw in the coolest air possible and exhaust the hottest air possible. If you can't use ridge vent, then pull off two of those box vents, open up the holes, and put power fans there instead. If you know what you're doing, wire them so that they operate from a single thermostatic relay, and put the extra thermostat in the "spare parts you will likely need later" box. Just don't put the fans downslope - they do the most good when they are as close to the peak (and as near the center of the house) as possible.
If you don't believe in doing it that way, argue your point with the manufacturers, but don't let your choice void the customer's warranty.
If you really want to do it up right, harken back a couple of generations and get them to put a whole-house fan in the ceiling downstairs, install double-hung windows so they can lower the upper sashes, put sufficient static venting on to accomodate the CFM of the WH fan and let 'er rip. And then ask them for the unused air conditioner so you can sell it on Ebay.
Just for the record, I actually do have a degree in physics.