If you know a burst/burn phase is coming up soon, like Titan Heart phase, then go out of your way when you feel it coming up to save it for that. Otherwise, general school of thought is to use your offensive cooldowns asap if it's a long fight. The benefit of trying to stack them is not better than the amount of time you'd lose not using them asap over the course of a fight. But yes, as said earlier, save them for burn phases.
If your dots aren't reapplying itself, that means you are clipping the dots, and your initial application is stronger than your reapplication, in which case the game doesn't overwrite the older one which is why it says, "... has no effect." E.G. if you had BfB on while you applied your first CT, if you CT again but don't have BfB on, it won't apply to the target because it's a weaker version.