When calculating payroll, one employee gets two cheques with some earning codes on one cheque and some earning codes on another cheque.
This happens when the option to 'print on a separate cheque' is selected on a timecard.
The calculate payroll process, looks firstly to the employee record to calculate pay from any values listed there. Then it goes to the timecard (if there is one) and if the timecard says to 'print on a separate cheque', anything from that timecard will go on a second cheque. If that option is NOT selected, then any code on the timecard will over-write the same code from the employee record with its values, on the same cheque.
The separate cheque option is generally used for vacation or bonus payouts that may happen at the same time as regular salary.