Since journal entries don’t have an item field, you’ll have to trick QuickBooks into doing what you want with a $0 transaction.  Since these are purchase transactions, I’d use a $0 check.  Start by creating a bank account called Clearing Account in Lists > Chart of Accounts so that you don’t clutter up your regular checking account with a bunch of $0 checks.  Then go to Banking > Write Checks, select your clearing account for your bank account, enter in your items on the Items tab with a positive amount and enter the expenses you've already entered with your journal entries on the Expenses tab with a negative amount.  Always put a Customer:job on the Items tab, put it on the Expenses tab only if was also included on your journal entries  Once you’re done, check both your Profit & Loss by Job (which is based on your chart of accounts) as well as one of your job costing reports to make sure everything looks correct.

As for the estimates, the Amount column is your estimate expenses and the Total column is your estimated revenue.  If you have a line that’s only for expenses clear out the Total column.  If you have a line that’s only for revenue clear out the Amount column.  If you have a line for both, put your expense estimate in the Amount column and your revenue estimate in the Total column.  You can use the Markup column to help you determine the revenue (you can use either a $ or % for markup).