The accounting page is set up so that each company has its own set of books. On the Accounting -> Accounts tab, it will show a list of all of your accounts. It is default to list all accounts for All Companies, and then you can also view accounts by company by clicking on the All Companies drop down.
This allows you to view only the transactions for a given company. It is also possible to create accounts that are only linked to one company. Create a new account (To manually add new accounts, see Adding, Editing, and Deleting Accounts or Subaccounts.) and then click All Companies in the the Link Account To section and select the appropriate company. This account will then only show in that company's set of books.
This allows you to have certain accounts that would only be on this company's set of books.
To set the Operating Account, You go to the Accounting -> Companies tab, select the company on the left and then click the Company tab. From here click Edit on the bottom right, and choose an Operating Account for that company from the dropdown.
This is done to link the correct company to the matching bank account.
Once the operating accounts are set, the system does it pretty much automatically, as most transactions will be for specific tenants and buildings, and will thus link to the company that owns that building. But for all transactions you have the option to choose which company it is for. The same for writing checks, if it is for a certain building it will default to that company, and you can change the company as you write the check as well.
You can also have separate operating accounts by building, to set this up see Setting Operating Account by Building.
As you create a new transaction, you have options to choose for which the Company the transaction is for, as well as which Building/Unit under the Site drop down.
Even if you only use one bank account, as long as you are choosing the correct company for the given transaction, you can sort the accounting page by company and the transactions can be seen separately.