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The term company means the different entities within your practice. For example, you may have a company for the main business, one for the partnership and perhaps one for the financial advising division. Each company has its own general ledger. This allows employees to select the correct general ledger for transactions to be recorded against when creating fees or entering receipts. Financial reports are produced by company.
Companies are set up and maintained by the system administrator using the Maintenance>Internal>Companies menu.