With flat rate pricing even the troubleshooting is done flat rate. Most problems can be diagnosed within an hour. So you have a flat rate for Level 1 troubleshooting of say $50.00 If the tech thinks it will take longer than 1 hour for him to diagnose the problem than this would be considered level 2 troubleshooting and might be a $100 These fees are for troubleshooting only. When the tech finds the problem he would then quote a price for the repair. There is demo software on the internet that you can download or request a copy that shows you how this works.
Keep in mind with flat rate pricing you will not always complete the task within the allowed time. This should be rare however. If it is happening too much then you would need to adjust the time to complete the task.
You should be completing the tasks in less time than is shown in the book most of the time. This will make up for the rare cases when you don't.