I've always gone by a base for writing a long manga and writing a short one is a very similar process.

Writing a plot for a long manga
Here are some examples.

In general, a long manga has an exceptionally larger space of time to develop than a short one. This gives longer manga the advantage of allowing a story history, you can write about basically anything with a long manga. Most girl-orientated manga begin with a blog of the main character written in square boxes that are inside the frames of the manga pages themselves. A typical start is as follows:
I am Sakura, I'm 9 years old this year and go to Orange Road Primary, this is my brother, he's a bit of a pain sometimes and it's my wish to one day stomp him out underfoot. This is my father, he's a sweet and gentle man.. etc

This blog will usually go for a few pages while the character's actions and scenes run in the 'background', it is often broken up when a new character enters and dialogue commences. Then the blog is no longer an introduction and switches to thought, which follows an entirely different format.

In boy-orientated manga stories often begin with a narration:

This is the Red Sea, many monsters live here, and a not so well-known little island with a maniacal sea captain trapped on it...

Most often however, long manga with an original setting these days begin with a simple note:

Arklain, Town of Chil'le

Writing script for long manga is difficult, since there are so many pages offered for you to fiddle with the important thing is to try not to put in too much information all at once. You have plenty of time to develop things for the reader, go slow. Failing that, you can always devote the opening pages purely to the history of the world.

This is Arklain, it is Age II, the Age of wars is in the long distant past and the people live in tenuous peace ruled by an iron-fisted Council. The rebels have already started their own movement however, and their leader is relentless...

To develop a long story it is very important you have your setting very very solid, even if it is based on our world. And it is also important to have solid characters if you intend to keep writing. It is alright to develop a skeleton first to see how the plot runs, but once you're in the thick of it you should keep focus on who your characters are and how they will react in different situations.

A few key differences in long stories and short ones. First of all, a long story is usually started off being open-ended, but I've found that if you know the beginning, rough progression and ending of a story it is much easier to write the details. Even if the ending was as basic and simple as: The main character dies. Once decided you'll find the process much easier.

Secondly, a short story does not always have much development and focus on the world and various supporting characters that appear, and often most of them don't use more than 3 characters. Long stories can afford much more but it is again important to know who your key characters are and their functions.

Third, you must remember what you are trying to convey. If you find yourself straying from your original path either try to steer back towards it or sit down and redevelop your story, don't let the manga run away from you.

Quick Fact: It is a lot easier to keep on track if you first define a main antagonist and a main protagonist (or two) so that even if other things happen in the middle (and they will since you want to develop the world and the characters) you can always go back to it and think 'What does this part of the plot have to do with the main antagonist/protagonist?

Fourth, always re-read what you wrote, if it sounds corny chances are it is. Always have someone proof-read as well, someone that is within your target audience.

Lastly, don't over detail at first for long manga, you'll run out of steam. Write about one paragraph about each chapter if you can and about a page for each 30 pages as you come to it in production.

Below we will use the Arklain as an example. But of course, only Age 0 is released here so that the current release doesn't become boring.

Arklain Age 0
The Age of Forming
Arklain is a man with great power but no title, the Land is in feud and he leads an army that would end the petty battles. He is not a happy man however, and during his 500 year quest, he encounters many betrayals and heartaches, and this manga talks about a few of them.

Chapter I
The Awakening
Arklain awakens in a desert, there is nothing around him, no footprints, no food, no maps or water. He walks on however, and does not seem perturbed. He eventually comes to an encampment of desert-dwellers, it isn't known how long he travelled for, but the customs are alien and he does not tell them his name (Reader doesn't know either). He begins to tell them a story, his story.