I don't get to play Unagi as often as I like... but my understanding is that Chimera Shot is your priority shot EVERY time it's up, regardless of when your sting is about to expire. I think Kill Shot is the exception, but that's based on the mob's health. Chimera Shot is a key part of the MM rotation. If you use it every time its up, you won't ever have to worry about your sting dropping. Now, I haven't read up on MM since 3.3, not sure if I've read up on it since 3.2 even... so I may be uninformed of the latest.
As far as addons go, you may find Watcher useful. I believe it was originally created for hunter rotations in WotLK, once shot clipping was no longer a concern from BC. I've played with it a little but found I'd rather try to master the WotLK MM rotation without an addon. Probably explains my low DPS output.
Looking at it now on curse gaming, it appears they've broadened the addon to be more useful for DPS classes beyond hunter.