One would need to know more about your banking transactions between companies and whether each company is setup as a separate database or if all companies are combined into one database.
If security isn't a concern, and the Chart of accounts are standardized between all companies, then placing all companies in one GP database makes sense. You would use a segment in your COA as a company identifier. You could then use GP inter-fund setup to automatically create balancing intercompany entries when recording entries across companies.
If your companies are in a separate database, you might consider the Nolan Intercompany because it supports bank transactions between checkbooks.
This isn't really a question that we can easily answer on the forum. If you are a partner, then I probably gave you enough to get started. If you are a GP end user, then you should contact your reseller so that they can evaluate your requirements and properly advise on a solution.
If you would like more information, send me a separate email and we can discuss your issue...mbufano@intellitecsolutions.com