Using invoicing systems to make it simple - While you can make up your own invoice or use a free template, it's often easier to use an invoicing system that offers more in depth features. Some invoice systems, like Harvest, offer the option to create estimates for big projects, keep track of multiple clients and send reminder emails when payments are late. Another option is Freshbooks, which offers similar features but includes profit and loss sheets, as well as trackers to help you manage your time.
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.