I have a vertical scroll series myself. What I do is work with a very taaaaall blank image file to create my thumbnails (the non-animation equivalent of storyboards).
Compare this thumbnail:
...with the finished episode here.
You'll see some differences between the two versions. There is one panel in the thumbnail that's not in the finished version, for one thing. I do make some changes here and there as I go along.
The downside of this method is that formatting for print would be TEN THOUSAND NIGHTMARES.
Some creators try to get the best of both worlds by vertically stacking comic book pages. That way, the comic is vertical, but it can still be printed without extensive reformatting. You do need to be very careful with your page layouts though, so that it works in both formats. I tried to do this at first with my comic, but found that it was too much headache for me, trying to make the storytelling work in two formats simultaneously. So I kind of gave up on the double dipping, and have been focusing 100% on the storytelling for my primary medium: digital.