Can each application have a separate merchant account?
We set up separate iTunes Connect accounts for the clients so that the client gets all of the info they need and also the money from Apple where applicable.

You would also need to set up Apple developer Accounts for each client (You get them to pay for their developer accounts) They can then add you to that dev account and you will be able to manage the provisioning, certificates and other things on their behalf but using your developer access account.

Apple documents this thoroughly here:


iTunes Connect Developer Guide