Hi Vicky,
Thank you for your question.
Yes, you can allocate salary for hours worked to different jobs using Weekly Timesheets.
That is, enter their hours per job in their weekly timesheets with the appropriate service item and their salary item.
This will allocate their salary between their jobs based on the number of hours entered.
Please ensure the tick box 'Use time data to create paychecks' is ticked in Edit Employee via 'Payroll and Compensation Info' tab, and also enabled in Preferences.
Hope that helps you.
Regards,
Michael