There are a number of solid programs to automate Multi-Company transactions in good accounting software and ERP programs. One of the best is Dynamics SL. Who really likes making lots of journal entries at the end of a month to keep balance sheets in balance by organization?
What I like about this one is that it works great on the Accounts Receivable side as well-not just General Ledger and Accounts Payable. It also is a module that not only is available without having to go third party or ISV (Independent Software Vendor), but is available in the less expensive Business Essentials option of Dynamics SL.
Dynamics GP has nice features for Multi-Company if you are mostly interested in having those transactions automated on the general ledger and payables sides. To get this to work well on the Accounts Receivable side, an ISV product called Binary Stream is required. This product is written in the Dynamics GP toolset and does what the Dynamics SL product does-namely allow you to keep multiple companies, with the same chart of accounts, customers, and vendors, in one database.
In both solutions having the same year end is required for organizations with separate balance sheets clustered into one database.
With Acumatica, the cloud-based ERP product that looks like Dynamics SL in a browser environment, the multi-company capabilities are strong but there is no fee or module for adding this feature-it is included in the design throughout the product.