I too, do thumbnails on paper - and write the actual script at the same time.
I do a written summary/outline of the chapter I'm working on - a "this happens and then this happens and then this happens" kind of thing - to know what is going to go on in the chapter, but there's little to no dialogue included, and no descriptions of how the pages are going to look.
Then, I take those notes, and I sit down with a blank piece of paper, and start thumbnailing. Beneath each thumbnail, I write out the first draft of the dialogue, as well as short notes to myself about what all of these stick-figures are actually supposed to be, so that I won't forget before I have time to do full-size sketches.
My thumbnails/script look a bit like this when I'm done:
(this example is from a oneshot I made a couple of years ago)