Well I got a note this morning asking me if I could explain how I use layers in GIMP. So thought it'll be best to show with an example rather than just write out a bunch of text.

Grab this PSD file
That's a photoshop file with the picture I've completed as it is here, but GIMP, SAI, PSP can read it.

And this PSD file is the one with just the lineart and background so you can try it yourself.

This tutorial is specifically for GIMP, cos that's what I'm using, but the concept should be the same for the other programs.

I recommend GIMP 2.6.11 with the Gimp Paint Studio addon installed.

You can show/hide layers on that to see why they are arranged the way they are, and you may recolor to try it out for yourself ^^ I'd love to see what you come up with.

Nothing fancy, just an example.

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Layers are awesome and can make your life so much easier if you know/learn how to use them, even without messing with the more advanced settings.
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Look at the layout in my example PSD file here
LINEART
NOSE AND EYES
SECOND FUR
BASE FUR
BACKGROUND
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I like to think of layers as stickers that I need to apply on top of each other in a certain order to make my picture complete.
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I draw my lineart on one layer in SAI, then I save the PSD file and bring it to GIMP.

Now I have a lineart layer and nothing else.
I've included a quick background for you, so you will have a LINEART and a BACKGROUND layer when you start.

Most of the time when you import layers like this, you'll see a little box around your lineart when you select the layer. This is the layer's size, and to help you color it, it is best to make this layer just as big as your image is.

Layer menu -> Layer to image size

Now your lineart layer will be just as big as your canvas.
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Press 'U' for your magic wand tool.
The settings should be as follows:

[x] Antailizing
[ ] Feather Edges
[x] Select Transparant Areas
[ ] Sample Merged

Threshold: 15.0

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Now go click on the area OUTSIDE your lineart. Thats right, select the area where you're not going to color. Did you get a pretty little line showing what you selected?

Good, go to the Select Menu, and select Grow. Grow your selection by 2 pixels. see that it goes in slightly under your lineart? This is going to prevent those ugly white pixelated lines you get sometimes.
Go to your Select Menu again, and choose Invert this time. This is going to select the opposite of what you have just selected, which means you now have your character's area selected.

Go to the Layer Menu, and make a new layer. Just accept the default, we dont need to go into details just yet.

Cool now there's a new layer over your lineart. Go choose a pretty color to color your kitty, and then shift+b or just click on the bucket fill icon.
Try coloring outside of where the selected area is and take note that you cant. Click on the area you want to color once.

Oh noes? what happened to my lines! EC!!!
Yep, this is to show you why layers are cool. Double click on that layer in your layer toolbox to rename it to BASE COLOR or something along those lines. Now click on it and drag it under your lineart, but before your background.
Isn't that awesome? Now you have your color under your lineart, thereby not damaging it as you color.

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Your layers should look like this:
LINEART
BASE COLOR
BACKGROUND
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I dont know, think he needs a bit more color.
Go to Select -> Select None. Make a new layer on top of BASE COLOR called Secondary Fur or something like that.
Now press P for your paintbrush or click the paintbrush icon on the toolbox (I prefer to press K and use the ink tool, but either will work).
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Make sure you're on the Secondary Fur layer.
Now go try to color that muzzle without going over the lines.
WTF EC this is hard! OK, go over the lines, go mad. We'll get rid of that in a minute.

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Your layers should look like this
LINEART
SECOND FUR
BASE COLOR
BACKGROUND
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There is quite a simple way to get rid of where you went over the lines.
Click on the BASE COLOR layer. Press U for your magic wand tool and click anywhere on your kitty. You should have the area selected that you had a minute ago when we base colored it.
Go to select and choose invert. Click on your Secondary Fur layer and either Cut or hit Delete on your keyboard. Yay, no more coloring outside the lines. You may have to go to Select and Select None again to get rid of your selection, sometimes is doesnt do that automatically.
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Prevention is better than cure though, so here's the other way to do it. Get rid of your secondary fur layer and make a new secondary fur layer.
Go to BASE COLOR, press U for your magic wand tool and click anywhere on your kitty.
Go to your Secondary Fur layer and enjoy hassle free coloring inside the lines. When you're all done, Select None.
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You got it now? good, cause now we're gonna color his nose and eyes.
Make a new layer for Nose and Eyes, select your paintbrush/ink tool and splash some color on it.

Now why else are layers cool? Check this out.
Go to BASE COLOR, select Color from the menu and go to Colorize.

Mess around with those settings, you can pretty much tint it any color you want. Same goes for the Secondary Fur.
Now try it on the eyes and nose layer. See it affects both eyes and nose and not just one of them. This is why we love layers so much, and try to do each color, and details such as eyes and noses on their own layer.

(If you used black or white you'll have to adjust the lightness option in the third bar in Colorize.)
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Well, I hope this has been helpful!
Good luck and I'd love to see what kitties you come up with.

Enjoy!
SAI/GIMP