Diane,
We use the Time Accounting functionality for entering all gross pay records for employees, letting JDE journalize Project Direct costs, Indirect costs, and calcing/distributing flat burden. These records are currently keypunched from paper (not using self service), although we are in the process of implementing a 3rd party front-end labor collection system that will feed the same F06116 table.
We then created a simple export UBE to create a summarized flat file from the F06116 (or F0618 History table) to present to ADP, which does all of our gross-to-net calcs & paychecks.
We also have the Time Entry proc options set to feed to WO Hours & Quantities on the Mfg side, although it sounds like you wouldn't use that piece.