For almost every zone beginning with the Heavensward zones, it is simply not possible to fly until you've finished the MSQ in that zone, and therefore it is not that big a priority to get all the aether currents.

For the aether currents that you have to interact with in the overworld, all are within 50-100y of an NPC or object that you have to interact with during the MSQ, so it's enough to ping your compass whenever you interact with an MSQ NPC or object and seek it out if it's less than 100y away. There is no need to go searching the entire map for them, and in fact there are several zones where it is not possible to reach all the aether currents the first time you visit anyway.

For quest currents in almost every zone, they are blue +Q quests that appear one or two at a time whenever you reach a new camp. These are good to do as they appear, to minimize backtracking.

The final aether current in all but one or two of the zones comes from the MSQ when you are done with that zone forever and ready to move on to the next zone. This is the limiting factor to flight. If you've done the four blue +Q sidequests and clicked all the overworld aether currents by the time you reach this quest, you can unlock flying as soon as it's done.