You extract the skintone and the eyes, then in Photoshop or another picture editing program you place the eyes on all the faces that come with the skintone. If you are using layers, you then need to flatten the image so that the file you end up saving is a BMP. You then import the skintone back in using Bodyshop.
I have no idea what skintone it is that you are editing. Also, keep in mind that regardless of the eyes you put on a skintone, sims will still use the normal Maxis (or default replacement) eyes. For the new eyes to override the normal (default) eyes, you need to make a default set using the eyes that you want, rather than just editing a skintone.
The four normal skintone shades will show the eyes that the sim has assigned to them and not the eyes on the skintone. The only ones that will show the eyes on the skintone are monster default replacements, eg. vamp, plantsim, etc. Replacing eyes on a normal skintone will not replace the eyes that a sim is showing. And to change monster eyes, you actually need to create the eye replacement on the faces, change the file type to PNG, then create a default replacement using SimPE.
If you are having trouble or want a specific monster replacement set, it might be easiest if you just make a request in the skintone request area of the site.
A couple of default replacement tutorials:
http://www.modthesims2.com/showthread.php?t=129993http://www.modthesims2.com/showthread.php?t=194390I really like the second one and it includes some templates (the 4 normal skintones and vamp)