WorkWeek will help you keep up with which invoices have been paid, which ones are overdue, and give you statistics based on your invoices, so it's important to make sure their status is kept up-to-date.
If you've enabled WorkWeek Payments, invoices that your customers pay online will automatically be updated for you.
You can update the status of invoices that haven't been paid online by first finding the job the invoice is for on the Jobs page and clicking it. Once you're on the job's details page, find the invoice under the ESTIMATES & INVOICES section and click it. That will take you to the invoice details screen, and from there press the blue popover menu button on the uppoer right and choose Mark Invoice as Paid.