When setting up the integration there are a few points you need to consider to know how you want to setup the structural relationship. Below are the few examples which may help you understand how to determine the structural relationship,
If you charge a flat rate for each project and there is no other method for charging your customer, the recommended practice is to setup the Projects in Web TimeSheet as an Item. The items in QuickBooks are used for adding onto the invoice. As you charge the clients based on per Project it is recommended to have the Projects as Items.
If you charge based on the Task performed for a project then the recommended structure is to have Projects in Web TimeSheet as Jobs and Tasks in Web TimeSheet as Items. As you charge the clients based on tasks against which time has been entered it is recommended to have the Tasks as Items and Projects as jobs.
If you charge your clients based on the user who works or the role needed to work on the project then you can setup Roles/Rates in Web TimeSheet and then the recommended structural relationship would be Project as Job, Tasks as Sub-Jobs, Roles as Items, as you charge the clients based on the roles or user rates.
Note: The above mentioned structural relationships are just to guide you in understanding how you can find out which structural relationship would suit you the most.