what are your two time sources?
GPS + PPS and RF-clock similar with DCF77?
(i don't know if, there where you are/live, a similar system exists)
do you want to use two PPS for failsafe or for increasing accuracy?
is your serial port of the GPIO connector in use?
i found that, where the serial port is mis-used to receive (non-standard-serial-conform) the time signal of the DCF77 module.
(de) - Raspberry Pi und DCF77 Empfänger von Conrad
(en*) - Raspberry Pi and DCF77 receivers from Conrad
(de) - Raspberry Pi als Funkuhr und NTP-Stratum-1-Zeitserver
(en*) - Raspberry Pi as radio clock and NTP Stratum 1 time server
*) translated version
then take a closer look to the Generic Reference Driver (8) of ntpd, maybe there is something you can use.
Generic Reference Driver (8)
or, if you have more than one RPi, then use them, where each is using one PPS-gpio and combine them via network:
should be ok when you combine those two stratum1 servers in the consuming clients
stratum1.server1(atom controlled) + stratum1.server2(rf controlled) ==> stratum2.client(n)
also for failsafe reason a construction of two different RPis would make more sense.
you can turn off one for maintain reason and the other is still working as time reference.