The reason I'm putting this up is because I've been asked the process of how I create my own manga, so:
Start with a storyline, plan it from beginning to end, don't start with just an idea or a beginning and just head off into the Manga from there, you can get lost in the story, slowly change genre, or even worse, the story just becomes boring... Plan the major twists and climaxes in the plot from the beginning. It is very easy to get lost in the middle of your story or get a writer's block...
Famous Manga works gained popularity from a great story, and not necessarily the best art, so don't worry about polishing your drawing skills to the N'th degree to begin with, if you already have a great story, start working on your na-me, your art will get better over time. Just have a look at your favorite Manga, see the difference between chapter 1 and chapter 100. Even professional Mangakas are still polishing their skill as they produce work that are published.
At this stage you should know