Ok here's an example of a recolor. Let's say you want to recolor Poochyena with Piplup colors.
Take a Poochyena sprite and place a Piplup sprite next to it for reference.
Then zoom in and use the color picker (the eyedrop thing) to copy the lightest color off Poochyena. Make a block out of that color. Then do the same with the second lightest color and so forth. Do the same for Piplup's colors and have all color blocks next to each other like so.
Now you replace all of the Poochyena colors on Poochyena with the corresponding Piplup colors.
Take out Piplup and color palette and tada~! A blue poochyena~!
Do the same technique when adding pokemon limbs in the "Pass the Sprite" game. By recoloring the limbs to match, you make it more believable.