System profiles should be seen as separate entities and there are no links in-between them. If an agent group is shared over several system profiles then the shared agent group and all that it is communicating with should all be in a single system profile. If there is communication taking place between the two environments it needs to be one system profile except if you want to follow the transaction from one to the other.
What is the reason why you would want to split up the agents into several system profiles?
If it is due to making the transaction flow simpler then you should look at the transaction flow in the web UI as you can group agent groups there.
If it is due to privileges you might want to vote for this RFE:
Thank you Mike. It's for a client that has 1 system profile which contain 2 environments; 1 is the internet website environment and the other is the backends environment that is handling the requests from the web site (users). Each environment is managed by it's own team. Client has indicated that they'd like to have a seperate system profile for each environment but without losing the coherence between the 2 environments. I'll have a look at the link you shared. Cheers.
A pure path in one system profile will not be found at all in the other system profile. If there is no communication between the two then that isn't a problem. But if there is communication taking place between the two environments it needs to be one system profile.