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 pay the employee based on the Employee type, the payroll item should be mapped to the Employee type. Based on the way Web TimeSheet is setup either the Employee type Name or Employee Type Description should be mapped to payroll item in QuickBooks. Eg: Full time hourly, Full time salaried.
If you pay the employee based on the Activity/Project they work against, the payroll item should then be mapped to Activity/Project Name or description. Anything that affects the users pay will be mapped to the Payroll item.
There are Payroll items for time entries and for Time off entries, so based on what they will be paid for while on a time off should be mapped to the payroll items for timeoff entries. Time off type can be setup as Payroll item if the time off type they book against determines their pay.
If none of these fit the criteria you pay your employees on, then you can use User Defined fields within the Web TimeSheet application to capture that data. The page on which this should be created depends on the requirement, if for eg. it is specific to the Employee then a Employee level User Defined field should be set, however if the payroll item is dependent on the time entered by the users then a User Defined Field at the timesheet level would be more appropriate.
You need to ensure that the option Use time data to create paychecks is enabled for the users. Once the application has been configured to capture the payroll items you can begin integrating Web TimeSheet and QuickBooks for payroll purposes.