There is no option available in QuickBooks integration Manager for creating different invoices for each user within the project, however you can achieve this by using the available filters and manipulating the approval status in Web TimeSheet.

 
First you can run the Detailed Task user report to find which users have entered time for that project. While generating invoices in QuickBooks you normally transfer timesheets that are approved, you can unsubmit timesheets for all but one user in the Web TimeSheet application for the date range you are trying to generate an invoice for. Once this is done then you can generate the invoice using the QuickBooks Integration Manager. Once this data is transferred then unsubmit the timesheet that was transferred and then approve a timesheet for another user and then generate the invoice again. Repeat these steps till all the timesheets are transferred for each user.