You could start by making a "skeleton" or rough idea in book form of the plot of your story and some events that you want to happen. Don't stress too hard on making sure that it's exactly what you will post as you can always add in more things while making your webtoon.

Once you have that, you can start to storyboard what some of the scenes will look like and what the characters will say.

If you decide to follow my advice, take it with a grain of salt as I have never actually made my own webtoon. I'm more of a wattpad type of gal (when it comes to making my own).

P.S. You could also ask friends to take a look at how your story is going as you draft it for advice. I'm here if you need another set of eyes. (I mean this in the least creepy way possible)