I figured you could use a Uniseal bulkhead (http://www.aquaticeco.com/subcategories/829/Uniseals) for the curved body or possibly go through the bottom plate of the skimmer.
Yea, a uniseal would be better than a bulkhead for this I agree. I really like the idea of going through the bottom plate though. That thing is flat and pretty rigid, so no worries about anything cracking. However, as long as you got it working Paul, I wouldn't mess with it.
As for the organization, I didn't see the before, but the after looks pretty good. (Well, maybe except for that rusting power strip. )