I'm not sure about others but the smaller parts I'll paint then put a red sharpie over the # on the sprue and on an index car write the # and color so when's it's cut from the sprie I know the color to touch up that spot..Also I build in sub assemblies; engine,interior, chassis etc. Then assemblies are mated in the order they need to fit together..

Hope it helps but I think every modeler develops their own process for this. That's part of the fun of the hobby, isn't it?

thanx and enjoy building..