I think one of the big issues here is of terminology. I
think that the "boxes" you're talking about refer to the individual panels of a comic page. When you talk about coloring "on-line," I'd assume that's the digital coloring step done in Photoshop, Illustrator, Paint Tool SAI, or any other art program on a computer (In that case, you're not using the internet and not actually "on-line").
As for the actual layout of your art, that depends a LOT on how you want to pace things and what kind of a tone you want to set up. Bear in mind that color is completely optional. You can get quite a range out of good o'l Black and White if you're just starting out and don't have a functional grasp on color theory just yet.
I'd recommend sketching out a couple pages of how you want things to play out first. Just play around with the first three or so pages, adjusting your characters, the focus of the "camera" and the rate at which you actually drop your dialogue. Finding the pace that's uniquely "you" is going to take time, and you're certainly not going to get it on the first try. Strive for a balance of action and atmosphere that fits the tone of a scene.
Example: a scene of two guys preparing their guns before a gun-shooty-type operation might take a few pages to linger on the firearms, the scenery, maybe a few dark profiles of your characters, and some dark scenery that'll give the dreary impression you're aiming for.
Alternativly, you could have those same two guys running in with guns a-blazing, while holding a casual conversation with each other right in the thick of it.
Think of your panel layouts as more dynamically framed movie storyboards. Think of the tone of a movie scene with the same tone you're looking for, and analyze each shot. When the camera jumps in focus, that's another panel that you'd draw (Not one-for-one, but you get the idea?)
Try clicking through the images in this handy tutorial here:
http://caporushes.tumblr.com/post/17257013411/sourceDon't ignore it based on the cartoon-y Disney stuff. These guys know what's up.
Now, when you've got the rough outline all figured out (figures placed, and dialogue spaced so that it'll fit into word bubbles), Then DRAW THAT THING. Draw your little heart out. The nicest, shiniest, pencil-on-paper art that you can muster (draw lightly, though). Leave the dialogue bubbles empty for now, that'll come later.
What you should have at that point is a first draft. From here, you COULD take the traditional route and ink over your work with a variety of brushes, pens, and quills that I'm not going to mention because I don't know JACK about that (look up "inking," you'll find some tutorials. It's worth a look.)
More likely, though, you should probably take that first draft and SCAN it. Don't take a picture, but use an ACTUAL SCANNER. The better the scanner, the better for you.
From there, you use a program like photoshop, or SAI (which is free) to digitally "ink" the scanned image of your work. This makes all your blacks blacker, polishes your lines, and makes everything look crisp and clean (or however you want). This is done completely manually, sometimes with a mouse, but usually best to invest in a digital pen tablet.
After you've got the black and white final copy, you add color, which I'm not going to mention, becuase there are THOUSANDS of great tutorials for digital coloring. Use them, but probably just stick to B&W for now.
Here's a nice little step-by-step process of how it COULD look:
http://fc08.deviantart.net/fs70/f/2014/027/d/9/bprd_115_pg_14_walkthrough_by_jharren-d741bce.jpgOr here for a bigger, cover-sized example:
http://fc07.deviantart.net/fs71/i/2014/021/5/7/red_walkthrough_by_thechamba-d734pin.jpgAnd to clarify: Your first few pieces WILL look terrible. Even if you can draw gorgeous still-life and have a functional grasp of non-anime anatomy, page layout is tricky business. You've gotta stick with it for a long time untill you produce something worth a damn. The hardware for these kinds of endeavors can also be fairly pricey. Don't invest unless you're serious. Start with a few 1-3 page one-shots for practicing pacing, storytelling, art and dialogue. Your big magnum opus can wait, and it'll be all the better because of that.
Practice practice practice. Learn the more accepted terminology (Western comic illustrators will be your friends here), and PLEASE look around. There are plenty of other, more informed opinions than mine out there. Just don't get so bogged down by researching that you forget to do things. Study from others, but only compare your work to your own, past work in the begining. With any luck, that's where you'll see improvements to be proud of.