What I did to change the appearance of my npc's and already existing families and townies might seem a bit tedious, but after a few times it went fast.
First I created the sims in "create a sim family" in game using any custom content such as warlokk's high-res meshes. After finishing the family, and giving them any sort of name, I dont move them to a lot or anything, I just leave them in the available families bucket. Exit game.
After that I open SimPE and then the neighborhood. I choose the sim surgery option and then replace the skin tone on the sim I wanted changed in game with the one I created in the first step. After applying changes, saving and exiting, I run the game and enter the lot of the changed sim (or if the npc or townie is on that lot) and have the sim change their appearance in the mirror for the changes to show up n game. (or use insimenator object to change the appearance of townie or npc on the lot)
Might want to take your sims shopping at this time to rplace the too small or too large outfits in the wardrobe
Oh, and the sim family that was created in the first step can be deleted. What I wrote was just a fast explanation of how I do it. Better tutorials can be found at
http://www.modthesims2.com with the use of SimPE.