To set the Operating Account by Company, see Separate Books by Company/Setting Operating Accounts and go half way down the page.

Each building's operating account defaults to the same as the company that owns it. You can see this by going to the Properties page - Clicking on a Building, then going to the Building tab.

If you want a different operating account for a building, go to the Building tab, and click on Edit on the bottom right corner. From here you can Select an Option for the Operating Account from any of your bank accounts. Then click Save on the bottom right corner.