To keep things clear, we at DOKKA differentiate between Organizations and Companies. An Organization is the larger entity, such as an accounting or bookkeeping firm, or a large company. An organization has clients or sub-groups. This is the account-holder in DOKKA.
The sub-groups are called Companies. A company has its own financial structure and books. It relates to the organization in that the organization either has overall control of the finances or the organization is responsible to keeping the financial books for the company.
If the company is a client of the organization (as opposed to a division of the same organization) it will have its own account with an accounting system. The ERP integration will be set up on the company level.