This is what I do for my series, Jim's Days:
-Research
-Jot down note on the major events in the story, rise, climax and all
-Determine the time span for all of this
-Add more details to the respective notes, like the actual story
-Research
-Break down the notes into the main events of each chapter, which in turn determines how many chapter's you'll need (I estimate mine to have around 30ish from this)
-Illustrate the characters and setting of the story
-Visualize the chapter and make a storyboard illustrating the events of your notes on a page
-Edit and reorganize the storyboard to your liking
-Make the comic :U
I find that making a story linear is kind of dull, I like to and plan on mixing and matching between certain time periods to deepen my story a bit, given that mine has to do with time travel and what not :U Also, other things to consider is that, from my own research:
-An arc for a mainstream manga series is normally 3-5 chapters long (a volume size) While western comics are more unpredictable spaning 10 chapters to an x amount without counting the tie-in comics
-Manga tends to be 25-45 pages per chapter while a western comic tends to be 20-30 pages
-Chapters follow the intro-rise-climax-falling-conclusion/twist formula while still keeping in line with the respective intro-rise-climax-falling-conclusion/twist formula of the over all story
And yeah :U Basically, I start from the bigger picture because this way, I feel, makes the story more consistent? :U