Hi Bandaru - within AUTODYN you can create a new user-subroutine project through the options menu. This will generate a collection of fortran files. Once you have modified the particular subroutine you're interested in and compiled the project it will create new autodyn.exe executable. Within workbench you then select which executable is called when the model is run (depending on what platform you use this varies, but for windows its simply done by right-clicking on Setup). Change the defined executable from the default to the new one created when you compiled your subroutine.
You can check the ANSYS ACT Application Store. They have an extension with which you can implement your subroutine in ANSYS Workbench. I hope they have something for AUTODYN interface also.