Not sure I can understand your problem. As far as I know you can achieve what you are trying to do, to have dot painted to appear for second or two or more. There is also Fade effect that can be applied along with few other options/effects. And by the way, do you work with video, GIF or you are trying to convert video to GIF?
Create new blank layer and paint on it then use timeline to set duration and effects like Fade. Layer with paint should be above video and drag it outside of video group with video.