There are a few things here that I would like to comment on.
Full scripts are a good way to work, long run and short run. I realise that they are boring, and that they are not easy to write, but one of the problems that I run into while reading webcomics is that too many of them feel like the writer doesn't really have that much of a clue about the details of the story, and is making them up as they go along. A full script helps solve that.
Winging it. Once I figure out that any comic other than gag-a-day or slice of life is winging it, I am out of there unless you have me by the beard for some other reason. There is a highly rated comic that I am positive is winging it, but it's too funny for me to stop reading it, as frustrating as it is.
Personally (and I realise that my idol, Stan Lee did the exact opposite of me), I can not write the dialogue after the page is drawn. I need to know what the dialogue is to know how to frame the panels, how to decide on panel size, and how to restructure the dialogue if needed. But that's just me.
My choice for scripting software is Comic Life 3, for the following reason:
I can write the script in one window, and drag and drop the images, captions, balloons, and even panes from other windows into the final product. Quick and easy.
Eagle
(Good tools!)