You should be using it whenever it is up, for now. Using it early and continuing to use it throughout an extended fight is much more effective than waiting until you are low or out of MP as the former makes your MP last much longer, whereas with the latter you will likely just run out of MP again.

Eventually you will get improvements to Aetherflow which will give you 2 to 3 charges of it with one use. When that happens, you will need to weigh your MP recovery vs. "wasting" Aetherflow charges as the skills that use it are very powerful.