http://www.reddit.com/r/DestinyTheG..._vanguard_rep_faction_rep_and_vanguard_marks/
So, there's a lot of confusion about rep and mark gaining, and frankly this is understandable.
Bungie have done a pretty horrible job in UI explanations of how stuff works, BUT, this is the Demon's Souls approach - it forces a community to bang some heads together and figure it out.
So, after getting annoyed at the systems, I'm compiling this quick guide to explain how rep and marks work.
First and most important, marks can ONLY, ONLY be obtained once you hit lvl 18. And even then, they only really start to kick in once you hit lvl 20.
18 is the minimum, 20 is when you want to start focusing on getting them, as that's when they become more widely available.
Patrols
Now, every planet has an "exploration" mission, where you're given free roam of the entire planet (within reason), and you will find that the planets are split into named zones.
Each of these zones is connected by a web of tunnels or paths if you will. Usually sped through on your Sparrow, they very rarely contain enemies.
You'll end up learning how to get to each zone of each planet in time.
Anyway, each of these "zones" on the planets have beacons. They can be found by hitting the touch pad on your controller to bring up your Ghost, and you'll see icons in the area that basically highlight where the beacon is.
Head to one to start that patrol mission.
Now, each patrol mission is begun usually by varying factions. No matter who gives you the mission, YOU ONLY RECEIVE REPUTATION FOR THE FACTION YOU ARE ALIGNED TO.
You will NOT RECEIVE ANY VANGUARD MARKS FOR PATROL MISSIONS
Vanguard and Faction Rep
Before level 20, you will only receive Vanguard reputation for EVERY patrol you do. Usually +10 rep. You will also receive rep for completing Strikes and handing in bounties (bounties unlock at lvl 4, consisting of "kill 100 enemies without dying" or "complete X strike" or "get X amount of precision kills - aka headshots - etc).
However, once you hit level 20, you can buy a class-specific faction item that you can equip whenever you want, that CONVERTS that Vanguard rep into that faction's rep.
So if I go do a patrol mission at lvl 20, with no faction gear on for my Warlock, I will receive +10 Vanguard rep. Great. If I do a strike, I get Vanguard rep. Great.
Now, if I head to, say, Future War Cult faction, and buy their Warlock bond item that can only be bought at lvl 20 (same for every class), with no rep requirements, EVERY time I do anything that would have gotten me Vanguard rep, like patrols or strikes, will gain me Future War Cult rep instead.
I WILL NO LONGER RECEIVE VANGUARD REP, AS LONG AS I AM WEARING THE FACTION ITEM AT THE TIME I GET THE REP.
If I un-equip said bond, for my Warlock, I will gain Vanguard rep again.
Marks
YOU ARE LIMITED TO 100 MARKS A WEEK
And the best Vanguard gear needs 150 marks per item so...enjoy the grind people!
Marks cannot be obtained through patrols, unlike in the beta if memory serves.
Marks can ONLY be obtained via a few methods.
Once you hit lvl 18, you unlock the Strike Playlist. This shows up on the navigation menu in orbit, next to the Crucible option in the bottom right.
There are 4 playlists. One for lvl 18, 20, 22 and 24. All this is is a Fireteam of 3 like any other Strike, but you get put in to a random strike, REGARDLESS OF WHETHER YOU HAVE COMPLETED THE STRIKE OR NOT (so if you have yet to explore Mars, you may get thrown in to a Mars strike).
The lvl 18 strike gives you no marks, 20 gives you 2, 22 gives you 3, and 24 gives you 6.
These give you pathetic amounts of rep as well, ranging from 10 to 20.
At lvl 20, you unlock the daily heroic story and weekly heroic strike. The daily heroic resets, yep, daily. The weekly heroic resets every Tuesday.
Each have modifiers such as enemies do extra melee damage or enemies deal but are more vulnerable to certain types of damage like Solar for example.
The Daily heroic story mission gives you rep and marks, usually 5. Sometimes you can get rare material rewards, used to upgrade your rarer gear.
The weekly heroic not only requires you to be in a fireteam before starting it, but it gives you 3 marks, +150 rep and +3 Strange Coins (used to buy gear from the black market vendor that ONLY appears between every Friday and Sunday, with a minimum of 7 coins needed for each item he sells - and his gear is sweeeeeeeeet for sure - note that coins can be obtained via blue engrams as well as getting gold in public events, but they're not guaranteed).
[Edit] I don't know when this kicks in, but I literally just traded in 50 spinmetal after grinding some crates today to the Vanguard Quartermaster, and got +250 glimmer, I think 100 Rep, AND 5 Vanguard marks.
BEAR IN MIND - MATERIALS ARE USED TO UPGRADE WEAPONS AS WELL.
Materials
Now, materials found in the world during missions or patrols like Spinmetal on Earth or Helium vials on the Moon can be traded in to a quartermaster for PVP or PVE once you have 50 of the material of your choice.
Once you have 50 of, say, Spinmetal from Earth, you can run to EITHER the Crucible quartermaster in the Tower opposite the Crucible Master...guy...OR to the Vanguard quartermaster near the ship/dock area.
Depending on who you go to, you will get EITHER rep or marks (marks now confirmed) for Vanguard/your faction or Crucible, and glimmer, for trading in 50 materials of your choice. I think it's random as to whether you get rep or marks, but it may transpire that certain materials give a higher guarantee of one or the other, we don't know yet and testing will need to be done.
[Edit] See above under the marks section for handing in materials to quartermasters - seems like you can get marks this way as well.
Conclusion
So, here goes:
The best way to farm rep
Patrols and bounties as they're quick and easy, can be repeated however many times you want, and you can also simultaneously collect materials which can be traded in for rep and marks, AS WELL as doing the daily and weekly heroics that requires a fireteam already set up, otherwise you just go in alone and it's impossible (which gives you varying rep around the same value as a bounty).
The best way to farm marks
Complete Strike Playlists that you can comfortably complete with your gear, trading in materials, as well as doing the daily and weekly challenges (and the weekly challenge gives you strange coins for use of buying black market gear every weekend).
[Edit] Clichéd ZOMFGNOWAITHANKSFORGOLD...Thanks!
