You can certainly create multiple sites and we do not have any restrictions on the number of sites you maintain under one account provided at least one of your sites are LIVE.
Since ChargeBee's billing is based on the revenue generated each month, it will be calculated across the sites you have under one account. So you do not have to pay extra.
To create multiple sites under one account, follow the steps below:
Sign up for a new ChargeBee site here (with a different email address) and claim the site.
Email us the new site domain and the old domain that it needs to be merged with. We will activate the live site for your new domain.
You can then invite the email address that will be managing all your ChargeBee sites as an Admin. This can be done under "Settings → Site Settings → Users". You can also make the invited user the owner of the new site if needed in the same settings page.
When you log in to ChargeBee as the original user, you will see all your ChargeBee sites, and you can select the one you want to enter.