You could assign several company codes to one company as in the case which was briefly described in post for defining a company. This will help later in the consolidation where company code are under company.
IMG Path: Enterprise Structure –> Assignment –> Financial Accounting –> Assign Company Code to Company
After entering in the transaction, find the company code and enter already defined Company in the field next to it..
Save the entry and assign the configuration to related customizing request.
btw. You could also assign Company to Company Code from global accounting parameters, but this this way it is a bit more straightforward.