I'd use a table with UserID, Date, TimeIn, TimeOut, LunchStart, and LunchEnd as fields. LunchStart and LunchEnd would be left NULL for non-hourly-exempt employees.
Some might complain about the lunch fields being always null for some employees, but this is a pretty trivial concern. This is a very simple design that ensures one record per employee per day, and makes calculating total time worked per day very easy.
