I have a very good flash (Canon Speedlite attachment that cost me around $400-500) but the camera won't autofocus in the dark and I can't manual focus in the dark for the same reason. The subject is not visible until the flash happens. I can get it focused on a tree in front of me either way by shining a light on the tree, focusing, and then turning the light off (though I have to be careful if I leave it on auto it may get enough moonlight to decide to focus on the leaves of the trees behind the treetrunk I'm interested in). Then I wait for the squirrels to step into my camera's frame. This works great at and near the squirrel feeder.

When they're flying from tree to tree in the dark unless my camera is just accidentally focused correctly I can't see how to get a photo of anything except a little brown blur. Probably what I need is a lens with more focal length and less zoom.

The last problem is that they don't fly very much, so there's not a lot of opportunity. Maybe I should practice on bats. I know where they hang out, and they fly all the time.