Some interesting posts about ways to write comics using "visual scripts" in InDesign, and also another post about using Scrivener to write fictional comics at J. Abel's blog. I used Scrivener to write Ganges 5, and it went great. I highly recommend this program if you think it's the kind of thing you need. You can download a trial and use it for 30 days. Work through the tutorial that comes with it and you'll see how well-crafted an application it is. But it might be more than you need. If you're already writing a lot but your problem is organization and flow, then look at Scrivener. If you problem is you're not writing anything, you can probably just use a simple text app and get to work.