I think the general rule of thumb in extended fights is to just use stuff on cooldown and deal with the mildfires. You don't want to potentially lose a usage of a cooldown over the duration of the fight because you held it for too long.

I say 'potentially', because it's definitely possible that there's an encounter out there right now where holding cooldowns like that might be a net gain in DPS - but frankly it's a lot of work to figure out and I doubt anyone could tell you for sure just like that. On top of that these things are gear dependant too, as your raid gets more geared, bosses hit phase transitions faster and that can change timings very significantly.

Personally I just use things on cooldown and don't think too much, unless it's a really obvious scenario like Stone, Sky, Sea.