Please note that you need to use the below procedure for creating the customer account for the domains which is already exist in the control panel.
1> Create the customer account.During the creating of this uncheck the subscription option.That is dont create the subscription option.Now you have created only the customer account with out any domain.
2> Go to the domain for which you want to give separate control panel.Click on change subscriber.Choose the new customer name that you have created above.Click on ok.
Now you can able to access the customer account separately for that domain.Still if you have any issues,please update us.