Any positive transaction (deposit) you mark as Business is considered Business Income.
Business Income is part of the calculations we do for estimated taxes, so it should only include money that comes from your self-employed work. Generally, this is gross receipts or sales, including amounts reported on 1099 forms issued by clients or others for whom you provided services.
Other types of income you can report include any bad debts you recovered (if they were written off on prior-year tax returns) and interest on business bank accounts.
What not to include as Business Income:
Other deposits, such as a "regular" paycheck from an employer (as long as it has taxes taken out) should be marked as Personal. Personal Income transactions are excluded from the calculations we do for estimated taxes.
Also, any money you invest in your business should be categorized as an Owner's Deposit. For these types of deposits, select Transfer > Owner's Deposit in the Category list. That way, they're excluded from your taxable Business Income.