Your target load and whether it is earthed or has imbalanced impedances to ground will dictate common-mode noise seen on the line and, given that we don't know this, it's hard to guess. Be aware that just putting CM capacitors on the output of your power supply may sometimes be NOT the best way - it might be that your target load will perform better with capacitors to ground on some of its nodes. There is no general answer to this.
Not knowing the target load...
Not knowing the target load is a problem and on some applications I have had to get a supplier to remove common-mode capacitors on their SMPS offering so that I could effectively move them to the output lines of my target circuit. This was done to enable our target circuit to pass EMC tests without EMI currents passing through our circuit and causing problems.
Adding CM chokes to the output can be a mixed blessing
It can cause a slight increase in DM noise if the inductors are not perfectly balanced and the output capacitors are not perfectly matched. Personally I'd get rid of the CM choke. You can easily simulate the effects of course in micro-cap or LTSpice (both free) and this would become clear when you imbalanced the values.