Salary can include a Unit or not. That doesn't change what the Salary Pay will be. Most times, your State doesn't want you to show Hours, though. You might need to do this for Job Tracking = you want that salary allocated across the Jobs they worked on.
If the units are affecting the counting function for Vacation, you are using the wrong pay item or set it up incorrectly as a Vacation Pay item.
So, you need to: Confirm on your Payroll Items list what is the Salary Pay item. Edit the Employee name and put the Salary Pay item in their setting and put the Annual Salary here.
Now Use that item for their paycheck and/or the timesheet. Please see my attachment.