Billing hourly or per project
For hourly work, put your rate in the unit price and your hours in the quantity. For project work, use a single line per deliverable with a quantity of one. For retainers, set the quantity to the number of months covered. The description field under each line is where you make the invoice self-explanatory — "Homepage redesign, two revision rounds" tells a client far more than "Design work" and heads off questions before they are asked.
Deposits and partial payments
If a client has paid a deposit, enter it in the amount-paid field and the balance due recalculates automatically. The invoice then shows the full value of the work, what has been received, and what is outstanding — which is clearer for both sides than silently invoicing only the remainder.
Getting paid on time
Set a specific due date rather than writing "net 30" and leaving the client to calculate it. Put your payment details in the notes or payment information field so nobody has to email you asking where to send money. Number your invoices sequentially — it makes your own bookkeeping straightforward and looks more established than a random reference.