Yes you can.
Individual job's can be discounted by adding a discount item under the jobs Quotes & Invoicing item list.
To do this:
Open the job you wish to discount
Go to the Quotes & Invoicing Tab
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