The Mugen Fighters Guild

    what you want to do next is add new colors to the palette (These will be the colors used for the new separations).
    -first you want to find empty boxes in your palette that aren't being used.
    (http://i.imgur.com/meWf4rt.png)
   -If you hold down the [shift] key while you have a empty box selected and move over a few more empty spaces> then click on a new empty box you can select a group of boxes.
    (http://i.imgur.com/qKwIQsL.png)
   -Next, we want to make a gradient of new colors using the empty pal boxes you have selected.
      -Once you have the empty palette boxes selected (I usually prefer 4 boxes per item), Click on the Interval of Selected Colors in Gradient button.
      (http://i.imgur.com/Szw6w7D.png)
     -First you wanna choose a Start Color for your gradient. I like to choose a light color that i know is not already in the palette (I like to add this color using the add to custom colors button) then press OK . 
      (http://i.imgur.com/gRJ9YpU.png?1) 
     -Next you want to choose your End color for the gradient. I like to select the custom color I added and then turn the Val down or you can just choose a black,  (http://i.imgur.com/gRJ9YpU.png?1)
      then press OK.
     -You should now have a mixture of colors (that you selected) in your previously empty palette boxes.
     (http://i.imgur.com/rFSnIw1.png)
Repeat step 3 depending on the number of colors that you want to separate.
    -Once you have achieved the desired pal for separation, click on the save the Current palette to a new file button.
       (http://i.imgur.com/penQyTD.png)
     *I usually prefer to save it directly over the current palette that I started out with (Overwrite).
    -Once the palette is saved, you can close the palette editor.
-Close the current character you have open in FF3, and then open the character right back the new palette should now appear on the character now (If not you might have to go into the character definition and add the palette manually depending on the pal.defaults and palette's name (the first number in the pal.defaults is usually the that you should be seeing, so make sure the first number in the pal.defaults is matching that of your palette's name that you have save and save the definition.) reload the character and the palette should be showing now on the character).
(http://i.imgur.com/J0D87Qq.png)

Once you have the character opened with your desired color separation palette, go to the sprites left panel and press the Open the Image Editor button.
(http://i.imgur.com/vvjPmvp.png)
    -When the editor comes up, you may want to learn a few hotkeys for quicker editing while in the image editor (most hotkeys are similar to other image editing programs.) Here are a few Hotkeys.
[Hotkeys]

Spoiler (click to show)

Zoom in -  [Shift] + [Ctrl] + [plus]
Zoom out- [Ctrl] + [minus]
Actual Size-[Ctrl] +

• 
  Save -      [Ctrl] + [Skey]
  Undo -      [Ctrl] + [Z]
  Redo -      [Ctrl] + [Y]
  Select all- [A]
  Copy - [Ctrl] + [C]
  Paste - [Ctrl] + [V]
  Move to next sprite- [Ctrl] + [Shift] + [right arrow]
  Move to back a sprite- [Ctrl] + [Shift] + [left arrow]
  Move canvas tool- [M]
  Pen tool- [P]
  Color Picker- [C]
  Eraser - [E]
  Paint Bucket-
  Remap Pen - [R]

-Select the Remap Pen
     (http://i.imgur.com/syYWtHF.png)

    -Choose the first color that you want to change by clicking on it, and right click on the color that you want to change it to.
     (http://i.imgur.com/XkQv4TS.png)

    -Click on the next line of color boxes under the remap pen and apply the next colors until you have the complete gradients selected under the remap pen.
    (http://i.imgur.com/mBtQgsg.png)

    -Once you have the colors that you want to change on the remap pen you can increase the size of the pen.
    (http://i.imgur.com/VUYb2Mc.png)

   -Now use the pen on the desired part of the image that you want to separate (you can right click to reverse the pen).
    (http://i.imgur.com/LVML1ri.png)

   -Once you change the desired separation on the sprite with the colors in you remap pen press [Ctrl] + [Skey] to save the sprite.
   Next press [Ctrl] + [Shift] + [Right Arrow] to move to the next sprite and use the remap pen again and keep continuing the process.
    (http://i.imgur.com/Tc7Zn1R.png)

   -When you get a good amount of sprites saved, you can close the image editor ans save the sprite sff.