Dear Paul,
External reference using internal clock is one of the FMC112/FMC116 application mode. When you pass a 2 to the application, the whole chip set is configured for this given mode. That argument goes down to fmc116_cpld.cpp in a FMC116_cpld_init() function.
Indeed it looks like writing a 1 to register 0 of the CPLD is the write you need to do. As far as our reference design is concerned, the CPLD register range is located at the address of FMC112/FMC116 star start's address + 0x920.
I hope that helps, and please let me know if you need any more information about that before I close the topic.
Best Regards,
Arnaud