Replace `overlay` with `insert_shape_at_point`

[jgostick]

The overlay function should accept a mode, which can be one of 'add', 'preserve', 'overwrite'. It's currently only doing 'add'.

[jgostick]

It also does not work in 2D as mentioned in #950 (which I will close)

[jgostick]

In fact, this function is pretty janky as it's written in pure python. It should be re-written as a generic version of the insert_disks_at_points function(s). Instead of passing in r, you pass im_to_insert.