Hi Azazel,
APFI0 is the pin that is the default for M Series for analog triggering (your PCI-6259 is an M Series board).
If you are trying to synchronize tasks, then it doesn't really matter if you trigger your analog input or your analog output, so long as doing one starts the other.
From looking at the Device Pinout in MAX for the 6259 you can see that APFI0 is Pin 20 of Connector 1, and APFI1 is Pin 20 of Connector 2.
All of the timing is the same for outputting 1 signal or all 4 signals.
Attached is a VI that I modified from the examples and it should help show how you might want to create a synchronized measurement that uses an analog trigger.
Regards,