How to add and manage AWS organization in AWS partner Master payer

Your customer should setup an AWS account as an Organization and develop their own OU structure. You should share you solution with the customer via PrivateLink, public ALB/NLB, etc. You should not add customer accounts to your Organization or master payer accounts.

Here is a link to AWS Prescriptive Guidance for managing multiple accounts: https://docs.aws.amazon.com/prescriptive-guidance/latest/transitioning-to-multiple-aws-accounts/welcome.html

There can only be one management account per AWS Organization. The management account is where the consolidated bill is paid from.

You could add your customer's AWS account(s) to your AWS Organization, but you would probably not want to give them administrator access to your Organization. If they have this, they can modify the Organization settings, or get access into your AWS account and/or other customer accounts within your Organization. You could provide them access to the root user of the individual AWS accounts that they own, if it is deemed necessary. You can also invite existing AWS accounts into your Organization, as you mentioned the customer had a merger and will be taking over another account.

I would recommend reaching out to your AWS Account team to have a conversation about what the best account structure would look like for your situation. They would be able to dive deeper and provide additional insight.