Scott,
I just looked at those photos, and it looks like the stock speaker locations in the dash will be easiest, and probably not all that bad. When I was speaking of being bright in the dash, I was talking about general passenger cars where the speakers are very close to ear level.
You'll probably wanna make your own bracket too, instead of buying the ones from the above site. I don't know for sure, but I'd guess that you'll be better off mounting the tweeter below the woofer if you go with the dash. Also, try and seal around the back of the speaker with some insulation and it should help to create a tigher/more pronounced midbass.
Still better would be kick panels, but they would probably be pricey to have fabricated... unless you know how to work with fiberglass
It doesn't look like Q-logic makes any prefabbed kicks for Jeep Wranglers.