In one account has multiple companies, you will find option to select Company in each transactions. While most of the records (mostly transactions) will be separated based on Company, there are few masters like Item, Item Group, Customer Group, Territory etc. which are common among all the companies.
If you have separate teams working on each company, you can restrict access of the User to the data of specific Company. Click [here](/docs/user/manual/en/setting-up/users-and-permissions/) to know how to set permission rules for giving restricted access to the User.
A separate Chart of Account master will be set for each company in the ERPNext. This allows you managing Accounts/Ledger master separately for each company. Also it allows you avail financial statement and reports like Balance Sheet and Profit and Loss Statement separately for each company.