I only save Aetherflow if I am not in trouble with MP. Otherwise I drain three times and then activate Aetherflow again.
As Ryuko said, it depends on how well you know the fight. Titan EX I really want to make sure I have a stack saved for SS and some lustrate if we have troubles topping off the tank before MB.
On Garude EX I find myself using it for Drain more than anything else (also since drain does some nice damage on spiny after Garuda Jumps).

In the end it comes down to how you play an encounter. You'll get the hang of it for sure