EMG orients their pickups so that the logo reads correctly. I'm pretty sure they generally use blades in their passives instead of polepieces. It won't matter a whole lot which way it's oriented, if that's the case.
It's not really generally true that one coil is significantly hotter than the other. There are slight differences because they use different types of magnets, etc., sure, but not enough that you'd want to spin that pickup around in order to get hotter performance out of it. Besides that, the closer to the bridge you get, the LESS signal is generated, so even if the 2 coils had significant differences, you'd still want the "hotter" one closer to the neck... in theory... it's really not important, though. I think you're over-thinking things.
In any event, if you're not splitting the coils, the individual coil outputs aren't going to matter a whole lot. Unless my brain is totally out to lunch on me, a typical full humbucker has both coils wired in series.
Greg