laying one layer of glass, wetting it out, and then laying the second layer on top is the way that I typically do things.

It is true that it becomes a little harder to lay out with out wrinkels, but since the glass stays where you put it it pretty much comes out even. (you have to remember to lift and move rather than try to carress it into place)

Your current method (glass - wait - glass - wait) A) works, B) gives you a lot of control over how it looks. It's downside is that it takes longer, and (this is my suspicion, I have no evidance for this) it may cause teh boat to be slightly heaver.

epoxying two layers at once will also work, but with system 3, which is not espically 'runny', I have more problems with the expoy wetting out both layers, and often have to lift off the top layer to get the the bottom.

I also feel that you can ultimatly use less epoxy doing it this way. when placing the second layer, all you have to do is to lay out the glass, wait about a minute for the glass to wick up some of the excess expoy from the first layer, and touch up any of the still dry areas.

all of this is based on 6oz glass, you may have problems with the 4oz glass 'floating' on the surface.

Long and short of it is to use what will work for you.