Well, isn't that mutually exclusive? To make 3D layers appear in front of others based on layer order you have to manipulate the position, which is perfectly possible. Otherwise you can't have both. Your only other option would be to pre-compose each 3D layer and then stack the resulting 2D pre-comps, but naturally it adds a lot of extra work...
If you stick a 2d layer in between 3d layers, it will break the rendering order. But, as Mylenium asked, if you want to do this with every layer, why are you making them 3d in the first place?
Trying to use something other than position to organize your 3-D layers is possible but it is a bad idea waiting to bite you hard when you try to edit your project or render it.
It's the same thing with a 3-D app. There are always some kind of funky workarounds to make things appear where they wouldn't appear in real life but these "Tweaks" almost always cause more problems than they solve.