I was looking into replacing the meh-quality stock-pickups of my Epiphone Les Paul. I already have an LTD Viper to play heavy stuff, so I will probably be using my Les Paul for different genres, like post-hardcore, pop punk and alternative (think Underoath, My Chemical Romance, Bayside and Coheed and Cambria)

I was thinking about getting a Seymour Duncan Distortion in the bridge and a Jazz in the neck...what does UG think?
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I'd go with a Seymour Duncan '59/JB combo.
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The Seymour Duncan Hotrodded Humbucker set is a pretty good deal. a sh4 jb in the bridge, and a jazz in the neck. Or you could go for dimarzio.

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I find JBs to be really, really, painfully bright. Maybe a Super Distortion in the bridge and a PAF Pro or a SD Jazz in the neck.

The one guy from Underoath uses an SG with a JB.
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I love the tones I get for Coheed and Bayside with my Dimarzio Breeds and I would assume that they could do UnderOath tones since they work well for BFMV, Atreyu, and LoG.
I know Ray Toro uses a JB in one of his guitars, and the other has Phat Cats which are humbucker-sized P-90s. Personally. I'd look into one of these in the neck and the JB for the bridge.
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SD Jazz pups are great in the neck position, I have this with a SD Invader (as used by Tom DeLonge) in the bridge, they sound good both together too