There's only two sidequests for Aether points that are easy to miss if you're not simply doing all the sidequests, and they're both in Dravania Forelands. One is at the bug-men camp, and the other is the leader of the Tailfeather camp. Both require you to complete a prerequisite sidequest before you can accept the aether quest.
As for having to run around, that's a good thing. Forces you to learn the zone and deal with the hazzards before you can simply fly over everything.