I'll advise that you not mess with any of the palette that's already there, unless you just want to change something like a team color.
If you want to add new palette colors though, you can expand the palette horizontally (that's side to side, for our less knowledgable audience) by 3 pixels (preferably 3 so you can use shading) and then simply do the following.
1. Choose a color that isn't already in the top row of the palette and place 3 different shades of that color in the top row of the palette in the 3-pixel blank area you created.
2. Place 3 shades of the color you actually want to add in-game in the next row.
3. If you want the color to flash other colors, you can put them in these next 3 rows, but it's easier to just flip the 3 shades over so the darker shade flashes light and vice versa.
4. Place another row just like you did in step 2.
5. Place a row with the color shades flipped horizontally, or replace it with a color of your choice, which would also be flipped horizontally.
6. Place a row of greys just like for the other colors before it.
7. Same as 6, but with the golds now.
8. Same as 6 again, but this time with the blues.
Sorry if that's a little confusing. I'll give you an image as an example.
The color set on the far right is an example of adding 3 shades to the palette. The images in the bottom right show you what the skin would look like in-game in various states. Hopefully this helps clear up some of the confusion with this.