As you may already be aware, Survival is currently the spec of choice for raiding. This will probably change some time down the line(it has before after all), but for now, Survival is king. It is completely possible for a Marksmanship or Beast Mastery Hunter to top the charts when played well, but Survival is definitely best over all. Most likely this is because of the nature of the spec(s) versus the nature of the fights. I'll give you an example, albeit one purposefully picked to prove my point.
We'll look at Heigan the Unclean. Heigan, if you've never done that particular fight, is murder on your pet. You can keep you pet up through the blasts of green fire he'll enviably take, but you'll end up wasting a lot of your own mana and time keeping the pet up. I personally don't bother and just leave my wolf at my side. For a BM hunter this is nearly 50% of their DPS just hanging around!
And if you think this is a stand alone case, think again! Many fights are pet un-friendly and will cause you a lot of problems if you are relying on your pet for much of your damage. From Anub'Rekhan with his debuff to Ignis with his Fire, pets can be tough to keep alive and sometimes are just better off standing in the back with the hunter. This is especially true if you are using the new hunter's-best-friend, the wolf.
Marksmanship is more of a PvP spec, what with Silencing Shot and Chimera Shot. While I haven't played Marks in a while, from my observasions it seems to be burst-type spec, meaning that it can crit, and crit for huge numbers, but you can't garentee that it will happen and that makes it a shaky DPS spec, though that style is perfect for PvP. As I said before, both Bm and Marks specs can work as a DPS spec, but for the most parts these specs seem to be intended for other things.
The first thing you need to know about playing survival is that it's based off a priority system. This means your shots are given a number, and you'll shoot in that order. Here's the commonly agreed upon priority:
1. Kill Shot
2. Explosive Shot
3. Black Arrow
5. Serpent Sting
6. Steady Shot
Obviously you can't start with Kill Shot. Kill Shot is number 1 because if it's up, fire it. It doesn't matter if your serpent sting has fallen off, or if your Lock and Load just proceed. Kill Shot is by far you biggest hitter and you need to shoot it ASAP.
Explosive shot is next. If explosive shot is ready and the mob is not below the 20% health mark, fire away. This is followed by Black Arrow, which can trigger Lock and Load (more on this later), then aimed or muli-shot, depending on your spec. Serpent Sting will follow aimed or multi. Your goal is to always keep Serpent Sting on the target, but don't sacrifice your priority to do so.
Steadyshot is last. This should be used as a filler shot and should never be used if it will "clip" another shot. This means that if cast time on Steady Shot is longer than the cooldown left on your higher priority shots, don't use it. You are better off simply auto-shotting until your cooldown comes up.
I hear you, there in the back. "But Gossamer, you're missing Arcane Shot". No, I'm not. Arcane spells are for Mages. Oh, and its also on the same cooldown as your Explosive Shot, which is much more bang for your buck.*
So, that's your priority. Until Lock and Load procs, which it should because you just put Black Arrow up. So what do you do now?! Now, you change your priority.
Kill Shot is still top. If it's up, shoot it. Next is, of course, Explosive Shot. But don't spam it! What you want is a nice spacing so you don't override the secondary damage on the shot, which takes .5 seconds to go off. There are several add-ons you can use to help track this, I've found that I can see it easily enough by the debuff. Here's the priority I use whe L & L has procced
1. Kill Shot (if it's up)
2. Lock and Load
3. Aimed or Muli shot (the Global Cooldown will help you keep from overriding L & L here)
4. Lock and Load
5. Serpent Sting if needed, Auto Shot if not
6. Resume priority (This should mean another L & L, though you could possibly have Kill Shot up, if you didn't fire it at 1.)
That's really all you need to know about what to fire when. Obviously there are going to be times when you need to use something I haven't listed here, but those occations should be rare. Just use your best judgment and you'll be fine.
*Okay, bad pun.