YOu will need to either make your own adaptor using FUL-1 and SPC module to connect your smartport to the pixhawk.:
Or you can get some pre-made cables from craft and theory - http://www.craftandtheoryllc.com/product-category/frsky-smartport-telemetry-cables/
Full details on how to connect and setup with pixhawk is here on the official wiki:
If you have any specific questions please let me know so I can try to help.