You want to take in water from the bottom and inject it with the bubbles above that point. The idea is to pull in water and then mix it with air and inject it into the skimmer body. If you take in the water/air mixture instead of just water, you'd probably lose efficiency and possibly performance with the skimmer.
Just my thoughts. I've never seen a recirc skimmer set up other than drawing water in from the bottom and injecting it with the air higher than the point where it was taking in the water. So, if it were any better the other way around, I think we'd be seeing it done on the recirc skimmers being sold now.
-Joe