For the first part of your question, one JTS with multiple CCM instances:
The friendship between each CCM instance and JTS is automatic when you register the CCM application.
You would need to create friendships between the CCM applications manually.

If I understand the second part of your question correctly, you are wondering how the friendships get set up with multiple JTS each with it's own CCM.
In that case all friendships would need to be configured manually.

The part I am not sure about is exactly how the friends relationship needs to be configured (I am curious to know as well)
Is the friendship required between just the CCM applications or both the JTS and CCM applications?
And if it is both JTS and CCM does the friends relationship need to be configured between both CCM and JTS for each?
For example:
CCM <-> CCM2
CCM <-> JTS2
JTS <-> CCM2
JTS <-> JTS2

(hopefully I have understood your question correctly and I am not just stealing your post)

As far as I can tell, in case of CCM heaps (avoiding to name them clusters) with separate JTS, friends relationships would be needed between the different CCM in different heaps, to be able to access work items. See https://jazz.net/library/article/535 for an example.

You would probably need more fried relationships from a JTS to other applications, not registered with itself, to be able to access their data e.g. in dashboards. I remember that we had to do something like that in the 2.x to 3.x upgrade workshop.

In case you need to link an application like CCM to CLM data from applications registered to another JTS, you would need friends relationships between the CCM and that other application too, I believe. It is mainly some kind of trust that enables you to access that data, as far as I understand it.

My understanding is that the ccm server should only be registered to a single jts server,  and for any additional jts servers, they should register to the existing jts server.  
there can be n number of ccm servers registered to a single jts server.

However I am not certain  about how many jts servers can be registered to a single jts server..either we need to daisy chain the jts servers or multiple jts servers can be registered to a single jts server.