I'm also planning on starting a webcomic later this year (when I've got a bit more time to plan everything). I too am a bit uncertain about the best way to go about the writing stage.

From what I've read from established story-based webcomic creators, while there is no one right way there tend to be a few common approaches that I'll be using.
  • Flesh out the core cast of the characters before you begin. You don't need to plan every little thing about them, but you do need to make sure you've got a group that lead themselves towards interesting situations.
  • Have a rough idea of where you want to start, where you want to end (if applicable), how you will get there and how you want the characters to change. This might change as you go but it helps to have at least a vague idea of where you want to head so your story doesn't go around in circles.
  • Most webcomics seem to be based on arcs, which follow the above rules on a smaller scale. I doubt many webcomics plan all these in advance; you'll have some that might be critical to your story as a whole but many arcs can be put in or out of the story as you go.
  • Work on the script in advance. Work through drafts of arcs and ideas months or even years before they are posted on the internet. That way you can figure out what works and what doesn't before you put in the effort to drawing them.