I've been a project manager for 4 years and I have organized several businesses. From my experience, the best way to organize your business and stay on top of all the moving parts is simply to create systems. Write down every single process (or have your employees do it) and keep them updated.
Having processes your business will be efficient and you will save time and money (would you spend 2 hours writing down a process that will save you 10 hours of work every week?)
You will be able to:
- Track performance of all departments/employees
- Identify and eliminate repetitive tasks and bottlenecks
- Cut costs by eliminating or optimizing ineffective parts of your processes (those that don't give you a solid ROI)
- Manage risk: for example, having clear return policies on ecommerce will reduce refunds. Having contracts or work agreements will reduce the risk of being unprotected by providers or former employees.

Some of the processes you should create are:
- Hiring/firing
- Sales
- Customer Services
- Lead generation / Customer acquisition
- Accounting
Etc.

There are also a number of tools (both free and paid) that you can use to organize your business. For example, using project management tools you will reduce the amount of emails that your team will have to send in order to communicate with each other. This means saving time.

It's difficult to be more precise without knowing what kind of business we're talking about. But systematizing and creating processes is very easy and highly effective in all cases.
Feel free to schedule a call for follow up questions.