If it is all under a single payer, it is not supported to bring in only a selected few linked account / subscriptions. Cloudability is designed to take in multiple payer accounts/subscriptions because it uses both the API and the cost data exports available.
There is a Cloudability version that is specific to the provider in your situation, called Cloudability MSP. This would allow the vendor/service provider (MSP) to add their payer and then create Cloudability instances for each of their customers. It is similar in concept to the AWS Billing Conductor mentioned by @Graham Lea. The MSP would be able to configure what accounts or tags indicated it is specific to a single customer's data and your customer Cloudability instance would only contain that information.