Paying Salaried Employees while out on leave of absence

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How does everyone pay their salaried employees if part of their pay period includes salary pay and starting on their leave, it goes unpaid. Currently, we are manually editing the timecard flags for salaried employees to avoid the full salary from being paid.

Is there anyway payroll can be set up to refer to the date salaried employees are placed on leave to avoid payment on days the salaried employees are on leave?

If we update the assignment status to payroll ineligible starting on the leave date, they do not get paid at all because they are not pulled into payroll. If we leave them as payroll eligible but do not update their timecard flags to "Yes", they get paid their normal bi-weekly pay. If we leave them as payroll eligible and update timecard flags to be required, it stops the salary and we are able to pay for days worked. This set up is questionable, why do we have to update timecard flags for salaried employees who do not use timecards. Help