I'm not going to give you a definitive answer, but just thinking through this, my guess is that the vac/sick accrual is based on hours.  Salary is not based on hours, therefore it isn't going to work.  For example, when a salaried employee is terminated during the middle of a payroll period, you have to calculate what his "hourly" rate is, add that as an item and make your entry in hours.   If you want the vac/sick accrual to work, you will have to set your your item name to salary, but put the type in as Hourly Wage.   When doing the entry for the payroll period you will have to deduct the PTO hours from the standard hours so that the total hours are always the same.  In short, I don't think QB is designed to track salaried vacation.  It would be easier to track it separately in Excel or set it up as hourly in QB which is more hassle than it's worth.