Now that the budget or estimate is set up in QuickBooks, tracking costs is a matter of associating costs with items and projects. This is going to be a matter of using the items tab when entering expenses for sub-contractors, and using the item and job drop downs when entering time for employees. Once you start entering costs with items and jobs associated, your job based reports will come to life. You will be able to see actual vs estimated costs for every line item on that estimate.