Autopay for partial pay period

 We are investigating the use of autopay for our exempt employees. Our employees are paid on a bi-weekly basis and exempt employees would normally have 80 hours per pay period. 

We have a problem, though, with employees with a start date in the middle of the pay cycle. For example, with a Pay Period End Date of 4/26/13, an employee starts work on 4/24/13. JDE appears to create an 80 hour time card for all exempt employees, where the expectation is that this new hire should only get 30% of the biweekly amount. Does anyone have experience with this scenario? How is this typically dealt with?