Where should I input payments for the owners of the companies and the office employees who are all 1099

It sounds like you need to consult with an accountant about how to set up your chart of accounts. Owners are not 1099 subcontractors. Neither are employees. And the answers to your question depend on your form of organization. These are business organization questions and have little or nothing to do with Manager as an accounting package. Once you’ve decided those basic issues, if you have problems setting up Manager, then people on the forum will be glad to help.