You cannot currently reorder the images, but you can number the frame image file names sequentially in the order you want them before adding an animation to the atlas. Another option is to arrange the frames in a single image using a program such as Photoshop and creating a Tile Source with an animation that flips through the frames. This requires all frames to have the same dimensions, though.
Image names mirror the base name of the source images. This is currently an engine limitation. If you need to rename a frame, you can rename the source image file as a workaround.