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Open the Materials using the View or Window menu. You should see something like the accompanying image. This is where your tones, and panels, are stored.
I don't think many panel know about Manga Studio's provided panels, or how to cut those up into other panels. For now, I'll cover the basics of getting to the panels, choosing them, and putting them in.
With your Materials window, select Material, Default, Panel Materials. At that point you should see folders with names like "1 Panel Cuts", "2 Panel Cuts", etc. etc. If you don't, you're in the wrong area, installed your program funny/wrong, etc. I had an issue with the install of Manga Studio 3 where the panels, and many tones, just never showed up; Clicking on them gave me an error saying these files weren't where they belonged. My solution was upgrading to Manga Studio 4, which has slightly better tools all around. Maybe 3 works perfect for you, but if it doesn't, consider grabbing 4 or testing it out at a friend's place.
At this point, you need to count your panels on your sketch; Surf on down to the folder with the right-ish amount of panels. If you need more than offered, I suggest retooling your sketch or getting familiar with the Panel Rule Cutter. Using this tool and being on the right panel, you can snip and shape of one panel into two. If you have too many panels, but really hate the layout the others offer you, consider the ol' frameless panel trick; That means select a panel that, in some nature, is framed by the other, surrounding panels, and delete said panel itself. This is a trick I employ pretty often when I feel like layouts are getting too dull.
Go to the folders in Materials and find the styles for the number of panels they provide; 6 is as high as it goes, so be aware. The manga styles are actually what used to be known as "4 kouma" or "kouma", for panel, because they have, you guessed it, five--four panels. You're fucking me up, stop.
Drag and drop the style you want onto the page; It'll all become nice, neat layers for you. If things don't match, you can go in and select, drag, and drop parts of the sketch to be insde their intended box. Ta-dah; A layout!
Can't I Just Make Panels Myself with Layers and the Shape Tool/Create Panels Tool?
Yes, yes you can. Should you? That depends on how perfect you can make a square with this tool; Remember, the slightest tilt on the square or rectangle will be horribly obivious in the finished product, and could get cut off when printed if outside the blue box, as far as the shape tool goes. I've never toyed with the Create Panel tool, so I can't speak for it.
I use a digital means to draw directly onto my computer, which means a slight shake can make my square off; As my hands shake, sometimes, because they just decide to, this is a bad choice for someone like me to use to make panels. Manga Studio is a little more bitchy than Photoshop, and many times when you look at a finished page, even in 4, the image doesn't look as good as it will once you export it. Don't panic if you load a page and tones, especially whites, look grainy or in a low resolution; They won't once exported.
I Want to be New and Different; Can't I use Circles, Triangles, etc.?
Okay; Techincally, in the grand scheme of life, you can do this. Should you is another matter.
I'll be honest; I'm a layout and design person. A good layout makes something easy to read or use, like my comic or site, or the majority of comics and sites online. Bad ones are the ones that look bad, with things cramped together, or weird, different things used. . .just to be different.
Case in Point: I am an award winning layout designer. Not a very impressive award, mind you; I worked for Layout and Design on my high school year book for about three years. Believe it or not, all yearbooks, across the nation, get entered into a competition for the Best. Two of mine won this Best in Nation award, the third only failing as they changed the requirements and no one passed that information along to us (One pica is how off I was; A pica is a pixel. Imagine losing by one pixel on the margin!) The third, while it lost the final leg, still came in First (Which was just below "Best".)
Like most schools, our's had a newspaper; For whatever reason, Yearbook and Newspaper didn't get along. There was sort of an internal competition over whose publication was more important and demanded by our peers (Did you keep all your high school newspapers? How about the yearbooks? Yeah, I thought so.) At some point, someone on Newspaper complained about their layouts. To make the two groups friendly, I got sent down to their room to create a full newspaper of layouts. It took about a week.
Then the newspaper came out; The crew, having been upset about the squares I used ("Everyone uses squares!" they cried), had gone back and replaced all these with circles. While, sure, it was a. . .creative move, in layout, it was a bad creative move. The newspaper, whose layouts had always made reading the publication hard, had just taken their readers to a whole new level of "What the fuck?"
For a newspaper, circles are a horrible choice; Filling a circular space with text is somewhat of a challenge, and filling the space around the circle is more problematic. If you do a layout in all circles, you'll leave a lot of weird, white space. Like you see in the "circles" layout mock-up I provided.
The point of a layout is to make reading flow easily, and utilize as much space on each page as possible. Leaving big, open spaces of white nothingness means additional content must be print on another page, costing more. If your layouts are good and tight, you won't need to worry about having to print a page with a single image or article on it, or trying to come up with more content to fill that space. As you can see, circles don't sit tight against one another; They leave space unused for no other reason than a circle doesn't occupy, or can't, due to it's shape, the space in the edges.
Additionally, you're working in comics and manga, and aesthetics (Looks) are important; This is a visual story telling form. Aesthetically, circles don't make the page look very nice, reading-wise, it's a little confusing (Typically we tend to view things inside a circle as being isolated elements moreso than part of a line of elements, as with a story; Family Circus is a (popular? unpopular?) newspaper comic that uses a circle layout, but each comic is a single panel, isolated from the rest), and printing wise you lose money; Don't use circles. That's my advice; Use it if you will.
Bear in mind, readers can, do, and will stop reading a comic that, visually, is too hard to read. As cool and different as you might think it is, as you may want to be, it's highly unlikely readers will tolerate this in most forms. Tread down this path with caution.
But I Can Still Use Rectangles, or Triangles?
Other shapes with straight edges are fine for layouts; It's kind of cool to see how you can make this work. Again, though, I'd use a set of panels Manga Studio provides and then whip out the old Panel Cutter Tool. Want to see how it works? Look for an icon on the tool bar like your own; It should be near-ish to the top.
If you have this item selected, go onto the panel you wish to modify. For this, we'll change a tall rectangle into a set of triangles. You can be on any layer, but using one with art probably isn't a good move (I don't know if it could do something weird to it.)
Simply hold down your mouse button about at the area you want the panels to be separated. The mark you're making is the cut itself. You should see lines that come up and will twirl in any direction you move your mouse in, like those in the picture.
If you mess up, don't worry; You can undo it.
Keep in mind you may have text in this area later, so take care not to fill up every panel with art you can't bear to cut around; A character's face will probably need the most room, so bear your actual drawing, and finished page, in mind during this.
Let go of the mouse button when you get the position you want. You panel will change to something like the image to the right.
These panel cuts aren't permeate changes to the original panels file; That means the next time you go and select this layout, this cut won't be there. Feel free to play around with all sorts of fun results.
The panel creation tool is also under this tool option, if you click and hold on the tool icon itself; I don't make layouts this way, as I'm happy with the ones MS4 provided, so I can't offer in aid in using it. Odds are your comic layouts won't be terribly revolutionary; They don't need to be. That's your story's job.
Next, Inking Your Sketch.