You should get a consultant, is the best answer to this question.
All of your clients should trust the server certificate in ClearPass to be able to connect successfully. Alternatively, they can simply trust the CA that issued the server certificate.
The AD trust does not come into play with the certificate piece, depending. Unless that single instance of CPPM can today authenticate users of both domains, you might have to join CPPM to two domains specifically to authenticate usernames and passwords.
Those are just general things to look out for, but there might be many more depending on how you are setup and what resources your clients need to get to. Being that there are many details of your network that are unknown or that you cannot disclose here, you should engage a consultant who knows your network or TAC if you would like to try it yourself.