Hi,
I'm going to assume that you are developing in the LabVIEW environment; however, there should be equivalent examples in other supported programming languages if you are not using LabVIEW. You can output a 1kHz pulse train from one of the onboard counters. There are examples of this included with the NI-DAQmx driver that can be found in the NI Example Finder (in LabVIEW go to Help>>Find Examples). I would recommend looking at the example "Gen Dig Pulse Train-Continuous.vi" located in Hardware Input and Output>>DAQmx>>Generating Digital Pulses.
Another suggestion that I have for more robust synchronization, especially since you have multiple PCI-6259 devices, is to use the RTSI interface of the card to synchronize your boards. The RTSI connector allows for timing and triggering signals to be sent among devices in the same system. There are also examples available that show how to implement multi-device synchronization using this interface. They can be found in Hardware Input and Output>>DAQmx>>Synchronization>>Multi-Device.
Here is a link to good information about the synchronization capabilities of our M-Series devices:
Getting Started with NI-DAQmx: Synchronization in NI-DAQmxRegards,
Andrew W
National Instruments