running the sub with the magnet in vented means you have a slightly improved airflow and the coil(s) cool a bit better.
the other thing is that, if you run it with the magnet in the vented part, you will have a bit more airspace in the sealed part.
2 boxes with one sub in each is 3 dB louder than one box with a clamshell. this goes only if each of the combos receive the same power.
here  and here is all the info you need on isobarics.