Panels are used in manga to add structure and pace to the story. When creating one, you're basically creating a frame that will contain the action. While the actual creation is fairly simple, figuring out the best way to contain the action could be a little more demanding.
Read the script for the manga you're drawing since it will act as the blueprint that will shape your paneling ideas. If you are doing a traditional manga, consider constructing the page with the panels going from right to left.
Get a feel for what you are trying to portray, since the genre and writing style could determine how you make your panels. Is the manga a comedy, a mystery or both? Will there be a lot of tension or is it more in-your-face? Is it intended for mainstream audiences or can it be avant-garde?
Remember that there are six basic panel transitions used in comics: Moment-to-moment shows something happening in an instant (Panel 1: Man looking forward. Panel 2: Man looks over his shoulder). Action-to-Action is similar, but shows that something more physical has taken place (Panel 1: Man delivers a jab to a punching bag. Panel 2: Man delivers a right hook to a punching bag). Subject-to-subject shows that a little piece of time has passed between panels (Panel 1: Man fastens the guitar strings to his guitar. Panel 2: Man plays the guitar). Scene-to-scene shows either a change in location, or that a long passage of time has taken place (Panel 1: Woman walks down the building's corridor. Panel 2: A car is parked outside the building). Aspect-to-aspect shows something from a character's point-of-view (Panel 1: Woman looks up. Panel 2: A broken ceiling fan hangs over her [taken from her POV]). A non-sequiter is a transition that seemingly has no logical bearing (Panel 1: Woman sits on a chair. Panel 2: A lioness chases a gazelle).
Determine the design of the panel. If there is a scene with six people standing in one room, you're often going to want to put them in one long, horizontal panel to give the scene a panoramic look. However, if you want to give the same scene a more claustrophobic feel, you might put all six characters in a vertical panel. For establishing shots and big character entrances, create one panel that takes up most (if not all) of the page.
Assess the types of shots you can use. If a scene calls for an extreme close-up, that panel is not going to take up much room on the page. If a scene calls for a group shot (where a group of characters stand together in unison), you could probably put them in a mid-sized panel. In addition to that, the "camera" doesn't have to be pointed straight at the group. They could be at a three-quarter view or even have their backs to the "camera."
Portray dynamic scenes with fewer, bigger panels. If you are drawing a big action sequence that's going to last for a few pages, just use two to four panels per page. This way the action will be fast-paced, but the reader will have the chance to experience the intensity. If you are building up to an action sequence, use at least three to six panels (possibly more) per page to act as the "countdown" to the excitement.
Use mid-size panels (four to six per page) to portray conversations. Manga is all about drawing out the moment, be it two characters talking to each other or one character thinking to himself. A conversation in Western comics would be done on two pages with six panels each, whereas a manga conversation could last eight pages with four panels each.
Decide what is unneeded in the panel. Just because the script calls for a close-up, it doesn't mean you have to draw a mid-size panel with a character's face staring out of it. You could draw a small panel that shows only the left side of a character's face, giving the reader the opportunity to finish the panel in their mind.
Draw your panels using a straight-edge ruler so that they will look sharp and neat. The most basic panel is a simple square: two parallel horizontal lines connected by two parallel vertical lines.