If the 4 layer pcb has only the micro, supervisor and a couple of other chips it seems that 4 layers are probably overkill - if you can have a fairly good groundplane on a 2 layer board you'll save a lot of money and be able to combine both parts onto one board (unless you really want to separate the boards) and having two boards doesn't necessarily mean you'll be free of EMI and coupling issues - the interconnecting wires make good antennas. Many of my boards have micros and relays switching 240vac and they pass the CE heavy industrial testing all on two sided pcbs.
Don't believe just because you're using a 4 layer board that you won't have EMI issues. Also for CE testing, the more interconnecting cables you have the more problems you may have! Keep high frequency signals near a groundplane and filter any external signals!

One lesson I learnt recently whilst having a pcb tested for CE compliance - I had an externally fed 24vdc input so my circuit had a 30V transzorb and a polyswitch to limit the current in case the transzorb died. In testing the transzorb died so I had to add a MOV. So now the MOV takes the brunt and the transzorb cleans up the rest. Iused to think that CE was a pain in the arse, but now it has forced me to think carefully about how I protect my circuitry from the outside world.