My process is probably far too complicated, but it works for me, and depends a lot on my personal preferences when it comes to individual tools in various programs.
Manga Studio 4EX - all my storyboards/scripts are done with pencil on paper, but after that, they start their digital life in MS4EX. I create a blank multiple-page Story document with all the pages of the comic (if it's a one-shot) or all the pages of the chapter (if it's a bigger story). I then go about doing the panels and the VERY rough sketches (like, stick-figures and blobs) and the speech bubble-placement and all the dialogue. It's a first/second draft of the dialogue, but it gives me an idea of how much space this takes up.
Paint Tool SAI - I export to .PSD and open it all in SAI and do the cleaned up sketches. I prefer sketching in SAI because I'm used to it, it's got a nice brush tool and good re-sizing and transformation tools, which helps immensely since I tend to skew proportions and stuff when I draw. I know there are re-sizing/transform tools in Manga Studio as well, but I prefer SAI's.
Manga Studio 5 - once I'm satisfied with the sketches, it's over to MS5 for everything else. Inking, colouring, final adjustments, etc. I know I could do my panelling/speech-bubbles/dialogue in MS5, but I prefer the way the menus and tools and such work in MS4EX, and using 4EX allows me to do those multiple-page Story-documents - the basic version of MS5 doesn't have that.
As for the prep-work - the writing and researching and whatnot - it's a chaotic mess of reference-photo folders, story-notes in half a dozen documents, scripts/storyboards on paper, outlines scattered through three different notebooks, etc., etc. The weird thing is that it works perfectly for me, and I'm not sure I'd want to change it. XD