Once you set a fan profile in MSI AB, CCC gets automatically set to manual. As far as I know, there is no getting around to it. The only way to make CCC NOT do anything with the fans is to disable AMD Overdrive, which you cannot do as you are using the power setting. This is just another example of how CCC and MSI AB hate each other's gut.
If you set a fan profile in MSI AB, normally the fan speed from CCC will kick in first, but once MSI AB start, it will take over. Does not work always though. My advice (and is a bit of annoyance) is to set fan speed at about 50% in CCC and then set your custom profile at MSI AB. If for some reason MSI AB fan profile did not kick in, you will not cook your cards and you simply have to go to MSI AB and hit the user fan button once. I know, it is just stupid to have to do that - but what can I say - it seem the MSI AB creator inspite of being an awesome guy seem to prefer nVIDIA over AMD.
Are you saying CCC shows 0 and 0 for second card after you select it from drop down? I am guessing that is powerplay kicking in. AMD uses ULPS (Ultra Low Power Settings) that will put the second card to sleep when there is not a whole lot going on. I disabled ULPS in windows registry. So, powerplay kicks in, but both cards just drop down to 250/150 instead of one being 0/0. I will have to let someone confirm this though as I am not 100% sure about this.