I have done 5/8 bosses in Dragon Soul on heroic. I want to progress myself and my guild to Heroic Deathwing before MoP comes out, but I always have trouble on the heroic ship. Would like some tips on how to know when fire is actually out, (animation is supposedly bugged) and overall tips or secrets that might make this fight easier. Thanks
I assume you are talking about phase 2.
The strategy my guild uses (25 man) pretty much avoids dealing with moving from shadow/leftover fire in phase 2. We have our raid stand on the edge of the ship on the grey part, fires can not spawn here. Tanks in the middle and the rest of the raid should split evenly either side of Warmaster and the drake.
Raid collapses for shock wave and then runs back to normal positioning for roar. Raid members need to avoid standing in front of the drake due to breath when collapsing and melee should always be behind unless there is fire in which case either in-front(dangerous) or have the tank move to the side a little so that they can get behind the boss.
Controlling the fire is one of the key mechanics to the fight.
Throughout the fight as the ship takes damage, fires will appear, and the NPC crew of the ship will pour water over the fire. The mechanic of the fight is to stand in the fire while the NPCs are pouring water onto the fire - this causes the fire to go out.
If you do not stand in the fire while the NPCs are pouring water over it, then the fires will not go out.
Standing in the fire while the NPCs are not pouring water over it will kill you pretty quickly as it ticks for a large amount of damage over time.
Early on in Dragon Soul the fire did appear to disappear by itself, but this hasn't been the case in the last six weeks (at least) that I have been doing this encounter. (I am usually assigned to stand in the fire to clear it).
This blog post suggests that the encounter can be buggy which could contribute to the difficulties you have experienced. The blog also suggests some workarounds:
And further on: