Those are for different softtop frames. Which top do you have? The Supertop has an adjustable rear spreader bar that makes a Y shape that you can see through the side windows. The factory top does not (that's what the Quadratec version is for). Check out this link for an advisor tool: http://www.quadratec.com/advisor/jeep-soft-top
As for top qualities... for your year, Bestop will have the best quality. Their standard tops are a little better, mainly with the stitching and zipper, but Quadratec has a better warranty. Still, expect either top to last 5-8 years as long as they last past the warranty period. Bestop does offer the Sailcloth fabric, though... that's a thicker material that'll be a little quieter and durable. But, at a premium price, as well. If you plan on keeping the Jeep for a while, and don't want to worry about lubricating the zippers a few times a year, go for the standard Bestop. Otherwise, the price is hard to beat for the Quadratop ($450 vs $310 for upper doors and tinted rear windows). I wouldn't even consider the other brands, lesser quality (thinner materials)... Speaking as a former employee of Quadratec and dealt with customer service calls. 
Had to step out while typing my post and missed your reply. Sailcloth is a nice upgrade, but if you're content with the top you already have, you won't know what you're missing. It's the material used on 2001 and newer factory tops. Consider it if this is your daily driver and you plan on keeping it for a while (should last a little longer than the standard top, too).
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