The smog check technician will check the catalytic converters EO numbers. If they don't match the required CAT EO numbers for your car it will fail the visual portion of the smog check as an "emissions tamper".
Under the new regulation a pre-OBD II (pre-2009) converter can pass the smog check as long as it was installed before 1/1/09 and you can provide the smog station proof of the installation date. If however the installed CAT was not manufactured or approved for installation on your vehicle, it will fail the smog check regardless.
The following is a PDF by C.A.R.B. explaining the new California CAT law.
www.smogtips.com/Aftermarket_CAT_ARB.pdf