is it a wall quilt? Buttons aren't very comfortable to snuggle up against. Ask me how I know :)

If you are not using the buttons to anchor all three layers together, I would machine sew to top before sandwiching. That will allow you to use whatever color thread and be able to hide the thread ends.

I would sew them on by machine but when I have finished the last stitch I pull the quilt waaayy out leaving long threads before I clip them. This leaves enough thread to put through a needle and hide it in the quilt.
Welcome and waving from Colorado :wave:

Welcome from NE Ohio.