You can set a billable method and rate for your project in the 'Billing' section of the project overview:

There are three types of rates available:

By selecting a user-based rate, the billable amount will be calculated from the billable rate of each user. You can set their default billable rate on their profile in the Users tab.
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The billable rate set on their profile will be used as a default on all projects. You can override the default billable rate with a custom billable rate, project by project, in the 'Members' tab of the project overview:

If you bill time spent on different tasks at different rates, choose a task-based rate. You can then enter a different hourly rate for each task on the project's task list, like this:

Select this option if all time logs on your project will be billed at the same hourly rate, regardless of the task or the user performing it. Every hour tracked on this project will be billed by the rate that you enter here:

If you select this option, the billable amount will not be calculated from your time logs, and all time logs recorded on the project will be marked as non-billable.

If you will be invoicing a flat fee to your client, you can enter it on the project overview:

To create an invoice for a flat fee, you need to enter the fee on the project overview and add at least one time log to the project. Then you can issue an invoice in the Uninvoiced tab.

Please check this article to learn how to change the rates for new time logs only and keep the old rate for existing time logs.
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