One is the 'traditional' way, and you'll need to buy good quality paper made for drawing, pencils of different graduation, rulers and ink, aside from screentones and white corrector. The final result is something beautiful that you made with your own hands. If you want to publish it, you can scan it, and keep the originals.
But lately, going 'digital' has been the trend for the last decade. With a Wacom digital tablet, you draw your draft and then 'ink' it with the digital pen tools that just fill in with black where is needed. Of course, you can still scan your hand-drawn work, adapt it to the artboard in your screen and create a layer to ink it.
You can create your own manga using Photoshop, Illustrator, Corel Draw, the good ol' Freehand. It's a matter of adjusting the size of your paper, and whether you'd like to work with pixels or vectors.But if there's an specific program designed to create professional manga and print it right away for submission, or export it to a digital format to publish it as an ebook, it's Manga Studio.
Manga Studio comes in two versions, Manga Studio Debut, for beginners and Manga Studio EX, for professionals or dedicated fans who know what they're doing. There's barely differences between them, just that the interface for one is easier than the other.
The most current version is the 4.0, and there's still no info on when version 5 will come out.