Individual job's can be discounted by adding a discount item under the jobs Quotes & Invoicing item list.

At this stage any discounts must be a fixed dollar amount. 

To do this:

Open the job you wish to discount

Go to the Quotes & Invoicing Tab

Click the add item/service button to add a new item

Add the item as shown below:

1. Set the item Quantity to -1 (Negative 1)

2. Set the Item name / code to Discount, etc

3. Set the Item price to the discount you wish to provide

Hit Save and you're done!