You can enter an alternate pay rate on the pay entry screen.

Page 3 of this document, section "Individual Time Entry" shows how.  https://learning.myisolved.com/library/documents/68  (you must be logged in to view.  Log in first to isolved, ).

Once the rates have been entered, the Individual Time Entry screen will display the alternate pay rate name and amount in the Override Rate column. The hours will display in the Hours column. 

This excerpt below is from the document (without photos).  If the employee commonly gets an alternate rate, we can set that up in the employee profile (or you can).

Individual Time Entry To enter an alternate pay rate on the Individual Time Entry screen, the user will enter the number of hours in the appropriate earning column and there will be a separate column called override rate. If the employee has alternate pay rates setup, the user may use the down arrow and choose the rate. The other option would be to just manually enter the override rate in the field. If the employee has additional hours for the same earning, Ctrl+Insert may be used to add a row for more hours to be keyed. 

Once the rates have been entered, the Individual Time Entry screen will display the alternate pay rate name and amount in the Override Rate column. The hours will display in the Hours column.