Hi Dan,
The configuration for X.509 certificate based SSO between SAP GUI and SAP ABAP is fairly straight forward. Once SSO client installed, you can find your certificate from the SSO client UI directly. The rest steps are exactly the same as a scenario with a SSO server.
You can follow this implementation guide below.
http://scn.sap.com/docs/DOC-40145
Cheers,
Chenyang