I personally just animated the collisionPolygon at the same time as the sprite itself. I hope there is a better way of handling it though. Not sure if adding the collision as a child of the sprite would work; since when animating the sprite the collision should move with it - but I have not tested this yet.
To add more animation properties (or whatever they are called);
After you have the animation window open (at the bottom) navigate to the collisionPolygon2D and click the + button at the right of the properties you wish to animate, in order to add it to a frame. That should add them to the animation window.