For AoE rotations, I personally use one from another BLM Rotation thread that I'm having trouble finding but its basically this:

Fire 3 > Fire 2 ... (until around 1000 mp) > Flare > [Transpose > wait 2 seconds after first mp tick > Flare > Fire 2 > Flare >] repeat

I personally love this. It seems weird cause of the wait you have for the 2 seconds, but if you do it right, when you cast Flare you will get an MP tick right after which gives you enough MP to do Fire 2 and another Flare. By the time you finish that second Flare, Transpose is off CD so you repeat the whole thing. Using it real time in places like WP, mobs melt like crazy so just thought I'd share this one.

About the Fire 3 procs, another reason you want to use them right away is because if you don't, you effectively zero out the chance of getting another Fire 3 proc. I don't really have a problem with waiting for Fire to hit before seeing I have the proc, I will just wait until after my next cast of Fire before using it.