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"The only thing that confuses me is when looking at the budget."
Good observation. A budget just deals with items of income and expense. Because payments for the principal amount on a loan liability are a reduction in both cash and the liability amount (both balance sheet accounts), you need to set up a cash flow forecast to see the effects on your cash balance. QBO has a good cash flow planner: Dashboards > Planner. It will pull in all bills and invoices that you have entered and you can use 'Add item' to enter other future cash transactions.