The best thing about using an invoice system is that you can track your time against the amount you're getting paid for each task. In order to run a successful business, you want your hourly rate to be profitable so you're not losing time and money. Another benefit of using an invoicing system is that you'll never save over an invoice and lose the work you've calculated for another client.
Be transparent – Your client wants to know where their money is going, so don't hide or be too general with line items on your invoices, and be prepared to show receipts. Otherwise, they'll wonder if you're padding the bill. Be specific. For example, instead of listing "materials" as a single expense, list each one on its own line, such as: paint, nails, plywood, etc.