Right now the main thing holding my rogue back is how I'm using my energy. I have a 31/20 build using a sword MH and dagger off, with the 5 piece NS bonus, but I don't fully understand how energy works and how best to use it in PvE.

Typically in a fight I'll use an SS to open, followed immediately by a Slice and Dice (I have 3/3 imp S&D). I'll then use SS until the S&D is about to run out, at which point I'll reuse it. I'll follow this pattern to keep it up at all times, and use Eviscerate in between. The problem comes with the fact that I don't really know if this is the best thing to do - though I strongly suspect that it isn't given that I often have left over combo points.

There are also times where (Just pulling some numbers out of my ass to give a general idea of the situation) I'll have 11 seconds left on a S&D and 4 combo points on a mob, so I'll get another SS in, Evis, then SS until the S&D is up, at which point I use it again - sometimes with only one or two combo points on the mob.

Is there a better way to do these? Also, would rupture be a better use of the extra combo points? Any help would be great.

If you respecced to 20/31 your combo point generation would be a lot more predictable, and you could start working out some routines. But I guess you're waiting for an offhand sword.

5SnD/5Rupture/3SnD is generally considered a very good sustainable cycle.

I went with 31/20 for the extra energy in PvP, which I do fairly often. I don't have any in weapon talents (right now I'm imp gouge/ss, 5/5 parry, 5/5 precision, 4/5 dw, 1 riposte), so the dagger offhand is the best I can get at the moment, and I'm willing to take any type of slow weapon for mainhand, since I'm a long ways off from CTS/AQR.

Why would you find the need to go 31/20 for extra energy for PvP if you're a sword rogue?

CS->SS->Gouge needs 110, as does CS+Gouge on mages. I admit I don't see the need for Vigor+5ns for pvp swords, though. One or the other.