Too often I still get asked questions like "When do I go Marksman Spec?" or "When should I stack Armor Penetration?" So I'm going to give you a quick run-down.
This late in the expansion most new hunters have access to enough gear to allow them to spec right into MM, but if gold is an issue or you prefer to progress through the game properly, start of as Survival. You will stay Survival until ToC at least. Then once your gear averages out to 232 and 245 ilevel gear, change to MM to increase your dps.
Survival Raid Spec
Marksman Agility Raid Spec
Armor Penetration vs. Agility
Survival hunter should always gem for Agility. Marksman hunters should also gem for Agility until they reach a passive Armor Pen. rating 750-800 (passive meaning gear only, no gems, no procs). Once one reaches that level, one can start gemming for Armor Penetration, as it will get one close to the Armor Pen. cap (1400) and be more beneficial than Agility. At this point Marksman hunters should also switch to a MM Armor Pen build.
Armor Penetration also affects MM shot rotation. When Armor penetration reaches around 450, MM hunters can drop Arcane Shot from their rotation as Steady Shot will do more damage (Arcane shot, being Magic damage will not benefit from Armor penetration, Steady Shot will).
For a more in-depth look at Armor Penetration and Raiding Specs check out the following guides on WHU:
Armor Pen vs Agility
Survival Hunter Raid Talent Build
Marksman Hunter Raid Talent Build
Marksman Hunter Armor Pen Build
Keep on Hunting,