You're right, it is pointlessly long!
Ok, this is the way I do it, but its by no means the only way...
I have all my bodyparts on the one layer, including eyes, each with their own individual weightmap and skelegons, then when i send it to layout, convert the 'gons, I parent (in place) the eye bones to the head and give control to the weight map - If you try this any other way, (ie with the eyes in another layer) you need to select the eyes click on bones at the bottom of the screen then hit p for properties and tell them to use the bones from whatever layer youve drawn them in.
If this doesnt work, send me the scene file + objects and I'll take a look