That's interesting. I replaced the suspension in my old ENO DN with Amsteel (basically same size as Whoopies) and didn't really notice any difference in the hang. I was never able to get remotely comfortable with two people in mine, even with the stock suspension. But that's just my $.02.
As for your question, you are correct that the original suspension lines went through the channel once, back through the channel, and the two ends were knotted together (and the knot moved into the channel). As for the knot to bring the two ends together, I believe it was a double fisherman's knot. The other knot into which the biner clipped was a slip knot, formed by making a loop in the line, and then passing a bite through the loop. Not sure if that makes sense, but I'll see if I can find a demo.
Edited: here is a demo of the slip knot that you would make in the loop for the biner http://www.animatedknots.com/slip/index.php
. This demo is a little different than what you will do because it is shown using the knot at the end of a rope, instead of the middle of a loop like you will be doing, but the mechanics of tying the knot are the same.