Can I use separate databases to track my companies?

No, all you need is a single database. Each Acumatica SaaS subscription is housed in a single database where you can track financials separately for an unlimited number of related companies and for up to 3, 10, or 20, or more stand-alone companies depending on edition. Stand-alone companies within the database allows you to decide what elements should be separated or shared between them, such as chart of accounts, customers, employees, etc.