Affliction Warlock is underrated by many people. Comparing all three specs by looking at sim-dps it seems to be pretty weak. But you have to be aware of several aspects. The damage of the spec increases with every add spawning during the bossfight. The buff uptime of "Deadwind Harvester" easily goes from 40 to 70% or even more. So does Wrath of Consumption which could be another 10% damage buff. Except Nythendra and Ursoc there will be adds in the bossfights we can make use of. Just keep in mind you have to hit them at least once to get these assist-related buffs.
Some tips:
Try to place your Soul Effigy clever. Seed of Corruption, Demonic Power and Soul Flame will be a huge ST damage increase if adds are standing/dying next to it. Know where adds will be tanked or ask your raid for fixed tanking positions.
Place Soul Effigy into the boss if you have GoSac.
Cast Seed of Corruption on your Soul Effigy to make it explode faster (stacked Agony) or cast UA before you start spamming with "Sow the Seeds".
Spread your Agony for more shards (even low-damage ticks should generate them).
If Bloodlust is used on pull, delay Doomguard/Trinkets for ~15sec so Agony has more stacks (worth it?).
Relying on several simulations, Harvester of Souls does about 1,6% of our total damage (single target). Because you have to "waste" 4 traits to get there, this may should be the last trait to go for. Three points in Shadowy Incantations increases our damage by 3(6)% (> Harvester of Souls).
My way would be: Seeds of Doom + Inimitable Agony -> Soul Flame -> Wrath of Consumption
Soul Flame:
This trait gives you a lot of AoE damage, especially in dungeons.
Try to kill adds next to your Soul Effigy to increase your ST damage.
It does double damage with "Deadwind Harvester".