Hi Sam,
If you want to authenticate again ABAP using SNC you have the option to bind a profie to a backend application: please refer to chapter 6.2.3.2 Applications and Profiles of the implementation guide.
This configuration is made in the Secure Login Administration console and is download with the group policy.
BTW you now can access the SAP note http://service.sap.com/sap/support/notes/1970832.
KR
Valerie