Base Colors:
Save!
Ok, for the purpose of this tutorial, I'm going to use Cherry Blossom's colors and symbol. Because she is all kinds of awesome. That's why.
Ahem, I make a new layer under my "Inks" layer and call it "Body". I plan to set the base color for each part of the pony (body, hair, eyes, tail, etc.) on a separate layers, since it makes it easier for me to select them later on in case I need to make changes to them. This is especially useful if you're making customized "adoptables".
I select my "magic wand" tool (W)
and specify the following settings: 
New selection -- Tolerance: 10 -- Antialiased unselected -- Contiguous selected -- All layers selected.
Now when I click on the body of the pony, a selection appears (also known as marching ants). But not every part of the body was selected:
To add areas to our selection, I hold down the Shift key. A little "+" will appear right next to the magic wand indicating that its in "adding" mode. So I click on the areas I'm missing (legs, face, ears). If I happen to add an area I don't want, I either click "Ctrl+Z" or hold down the "Alt" key to "substract" from the selection. Just an FYI: If you hold down the "Ctrl" key while using the magic wand, it puts it in "move" mode.
Once I have selected all the areas I want, I go to Select>>Modify>>Expand and select a number between 1-3 usually. This prevents me getting a white "aura" between my base color and my lineart.
This is how my color would look like without using the expand option:
And here it is with an expand of "3":
It doesn't take care of everything but its much less area to worry about.
As you can see, I have already selected a dark pink color for the body. You can do this by double clicking on your foreground color and moving the sliders until you get the color you want. Hit OK.
Making sure your selection is still going, hold down the Alt key and hit backspace. This is the shortcut for filling any are you have selected with your foreground color. The "long" way to go about it is to go to Edit>>Fill>>Foreground color and leave the default settings alone.
Ok, so I have my first color in but there are areas that still didn't get filled (shakes fist) and areas I don't want to have that color. First things, first. I take my brush tool, which should still have my "inks" settings and just go over those areas. Its important to pay attention in this step, it looks really sloppy otherwise.
You may have noticed that some of the color "bled" into the eyes. (That just sounds nasty!)
I select my Eraser tool (E)
in "block" mode (It will basically look like a white square)and delete the color from that area. Eventually I end up with this:
I lock the layer's transparency like I did with my inks layer.
Next, I basically repeat all the steps for all the other parts (Hair, tail, eyes, ears) : Make a new layer, select, expand, fill with color, fix. Until all the base colors are down:
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