Do you mean page layout, character creation, plot, script, drawing and/or publishing?
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Depends on how much you know about manga. Which genre are you writing in? Each genre will have constraints for who the main characters are (Doujinshi would be considered fan art, Shonen is for teen boys, Shojo for teen girls, ect) and limits on the plot (Ghost in the Shell doujinshi wouldn't have Magic Girls in it, Shojo is unlikely to include mecha and so on). Honestly, if you need any of this, you should either read more or reconsider your media : P
Personally, I'd start with a main character and foil/side kick(s). That leads to plot, which leads to script. Artwork starts with character sketches, then thumbnails of scrips (the storyboard), then full-page workups/art. After you get your first comic done is when you start looking to publish (online probably, or small press where you sell your own). If you aren't a professional artist, or at least well on your way to become one, a publishing house isn't going to help you at all.
Start with the "How to Draw Manga" series for drawing instruction, as well as reading manga to see how the art is used. You can buy special layout paper (or figure out your own-most of it is figuring out where the printing borders/margins are and what your shrinkage factor is because most art is created two or more times the final print size). A lot of manga will use pre-printed textures to speed production.