Good day, TFarrz,
You can create a service item for your hourly rate and create a different one for the excess time.
The next time you create a sales receipt, you can enter the quantity of each item.
As for the discount, you can turn on the option here:
You can also create a credit memo for your customer to use in the future. Check this article: Enter and apply a credit memo or delayed credit.
Let me know if you have additional questions.