Our system is organized as follows:
There are NDN IDs (what you use to log into the web panel).
These should be one per actual person. So if you're the only one who will ever be logging into the web panel, you only need one. If your clients are going to log in sometimes, they should create their own NDN ID at http://id.newdream.net/
There are accounts. Accounts hold plans on them and plans hold domains/users/etc.. Accounts are separate billing entities, so generally you would want to make separate accounts if different people/organizations are going to be responsible for paying for different plans you have.
You can through the web panel (Home -> Account Privileges) allow any NDN ID access to any account (or just certain privileges on that account).
Payment methods (credit cards, checking accounts, paypal accounts, etc..) are owned by NDN IDs (actual people), and can be associated with multiple accounts. You can add/modify/associate them at the web panel as well (Billing -> Payment Methods).
I hope that explains how accounts/logins/payment methods work a bit on our system!
As for the mailbox question, yup that's all you do. The names associated with the mailboxes are just for your own record-keeping and nothing else. You can set up email addresses at domains to go to any mailbox created on the same account.
So create as many mailboxes as you want on whichever plan you want and then configure the addresses how you'd like!