I find that the zoomed are a little too small for my comfort when it comes to ball python clutches. those tiny bins that came with it are for gecko eggs. I do know people stack their containers, but you need there to be at least some air flow around them to allow for even heating. You can always set up the containers, shove them in there, run the incubator for a few days and then check the temps in both containers and see if they are good temps.
As for urinating, do you mean leaving white urate in the cage or releasing a liquid of some sort?
Also as for how close the eggs can be, most of the time the eggs stick to one another anyway (another reason that incubator can be too small if the pile of eggs is an awkward shape). So the eggs can touch one another, although if they are not stuck together people tend to give each egg a little space so it can be removed if it rots.