This is not done as per SSID, this can only be done on specifc Access Points.
Normally, Once a LAP registers to a WLC, all the configuration for a LAP is done on the WLC. There is a built-in feature in WLC called RRM, wherein the WLC internally runs an algorithm and automatically adjusts the channel and power settings as per the deployment of LAPs. RRM is turned on by default on the WLC.
You need not change the channel and power settings for a LAP, but you can override the RRM feature and statically assign power and channel settings for a LAP.
For more information on how to manually configure the channel and power settings, Statically Assigning Channel and Transmit Power Settings to Access Point Radios .
we have a cisco WLC 2504 in our enviroment and use 3 SSIDs (internal with 802.1x, and 2 guest ssids).
Can we configure our SSIDs with diffent channels, for example internal with channel 11
guest1 with channel 2 and
guest2 with channel 6
Can't be done on a single AP and this "design" doesn't make any sense.
Let's say that you want this done in a single AP ...
You've got one AP configured with three SSID. Each SSID is purportedly assigned a channel: SSID 1 is channel 1, SSID 6 is channel 6 and SSID 11 is channel 11.
So far so good?
Ok, now what channel do you want active?
A wireless access point (regardless of manufacturer) is not the Starship Enterprise where you can "hail all channels". An AP cannot and will not broadcast on all channel. An AP will choose one channel and sit on that channel until told to do otherwise. So with your "design", only one SSID will be broadcasted.
So, the "design" you were told to implement cannot be done with one AP.
You can, however, have three APs and each AP broadcasting different SSID and each SSID is assigned a different channel. Why someone would want to do that? I have no idea but it sure ain't "best practice" due to practicality.