My rotation for a single target mob is:
Bio II > Miasma > Thunder > Bio > Fester > filler (usually Ruin except for the occasional Ruin II for blind) > refresh DoTs as needed, repeat.
The reason I use Thunder before Bio is because I figure if I'm going to have to wait on the GCD anyway, I'd rather the Thunder+Bio be 'closer' together in time left. (Since Thunder takes time to cast and Bio is instant, if you cast Bio first, Thunder will be a few seconds behind.) Please note, Thunder deals damage and also adds a DoT effect. Bio is simply a DoT, so the effects are comparable even if you are waiting for Thunder to cast.
If you are in a rush to cast Fester right away, you can always follow the typical "Bio II > Miasma > Bio" pattern others have listed, but keep in mind that if you use Fester on cooldown without using any other charges, you will still need to wait for Aetherflow to come back up before being able to Fester again... So doing it my way is never 'wasted' DPS. This is just personal preference, so it's really up to you... I thought I'd give you insight into why I do it this way, though.
For the pet... Unless you want to save your Enkindle for a strategic time, I generally pop all pet cooldowns (Rouse+Spur, followed by Enkindle) at the start of a boss fight to get the recast timers rolling right away for maximum DPS. If you are fighting a boss like Titan, you'll want to save this combination of abilities for the Heart... but you CAN pop Rouse periodically since the cooldown is so short... and you should. Feel it out.
For adds, I will get my DoTs up and Bane them to other targets before throwing Shadow Flare down. The reason I do this is because I want to give the tank time to position the mobs before throwing down a ground AoE. Also, I don't think Shadow Flare DPS is as important as the ticks of all the other DoTs going off first. If your tank is well-equipped and skilled, they will be able to handle this. If not, go easy on the DPS and throw down Shadowflare to buy you some time before spreading all DoTs.
You can also run up and Miasma II the mobs after Shadow Flare if you so choose, pulling out the maximum amount of DoTs you can. It costs a decent amount of mana, but mana really isn't an issue while killing trash. If there are a LOT of mobs, Tri-Disaster is sensible, but only if there are a LOT... otherwise single-target nuke until you need to refresh/spread DoTs again. When refreshing DoTs, always refresh and spread the DoTs from a target with high HP. If you choose a target with low HP, you might not get to spread before the target dies... wasted time
Kevee's comment above reminded me of this...
Note: whether you are casting Bane or Fester, you must wait a split second after your last DoT is up (usually Bio) before using the ability... because if you do it TOO soon, that DoT won't count in your DoT spread or you won't be able to get the max DPS from Fester. It's silly and frustrating but you'll get used to it.



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