I think you would go about changing eyes about the same way.
Anyway, if you want them to go to your default skins, I
think that your just replace all the numbers with zeros, except for the last one. You use 1 as the last number for the lightest, and 4 for the darkest.
1. Decide which skintone you want them to have and open it in SimPE (so that you can discover its ID).
2. The ID is in the XML and is called Family (or some such - sorry - but I don't want to open SimPE ATM to find out).
3. Copy the ID to notepad or some such.
4. Open the Neighbourhood where the Sim(s) is/are.
5. Open their DNA and change the dominant skin tone to the number you extracted.
6. Commit, save, etc.
I'm wondering, would this update the property sets and age data files? I was thinking that you would use that to change what they looked like. I'm not entirely sure about that, but I do know that is something along the lines of what you do to change a Sim's gender, though there are probably more things affected by gender than by skintone in game.