How to create and add video overlays like this?
The tool doesn't matter in this case. 

For some kind of artistic or individual approach I'd suggest use a light table or graphics tablet. Draw the shapes 20-50 times by hand to get some nice variation and place all the drawings on top of each other like classic/traditional animation does in the old days.

Otherwise you can either use:


Any kind of pixel or vector based graphics package (Photoshop, Gimp, Affinity Designer etc.) together with Premiere or After Effects for additional tracking capabilities
A 2D Animation package which allows to draw directly on the plates 
Or even Blender's grease pencil feature  along with its tracking capabilities