Rolfe,
The 6289 doesn't have any filters on the Analog Output, so the only filter delays you will have to worry about are on the 4461.
To synchronize the two devices, you have several options. I'll ignore the filter delay on the 4461 for now and come back to it later. First, yes you can use CLK 10 to synchronize both devices. To do this, set the reference clock source to CLK 10 on each device by using the timing property node. For this to work, you will have to have NI-DAQ 7.4 installed since CLK 10 synchronization support for the 4461 was added in this version of the driver. In addition to locking to CLK 10, you will also have to share a start trigger between the two devices. Since there is no trigger support for digital output on the 6289, you will have to use the 6289's ao/sampleClock as the do/sampleClock and start the digital task before the AO task. This solution is nice in that you can output at different rates on the two devices and still maintain phase relationship throughout time.
A second option to CLK 10, is to use the sample clock from the 4461 as the sample clock for the 6289. When using this scheme, you will need to start the digital output and AO task on the 6289 before starting the task on the 4461. This approach is a little more straight forward, but has the disadvantage that it forces all tasks to run at the same sample rate.
Now, we need to address the filter delay on the 4461. So far, the synchronization described above ensures the clocks are synchronized, but it doesn't account for the digital filter delay of the 4461. Depending on the sample rate of the 4461, this filter delay can be 36.6, 36.8, 37.4, 38.5, 40.8, 43.2, 48.0, or 32.0 samples (see the NI Dynamic Signal Acquisition Help for more detailed information). If you are running at a sample rate that doesn't have a fractional sample delay (or you don't care about the fractional delay if it's close enough for you), you have a couple of options. First, you can account for the delay in software by generating waveforms in the software buffers that are already offset by the appropriate sample delay. If you want a hardware driven solution, you can use a start trigger for the AO task on the 6289 and specify a delay from the start trigger of the appropriate number of samples. This can be done through properties under the trigger property node. Using the ao/sampleClock on the 6289 as the sample clock for the digital task will then delay the digital task as well.
If you want to get rid of the fractional delay, you'll have to use the CLK 10 synchronization approach as well as a counter to offset the start of the generations on the 6289 by the appropriate amount. To do this, you'll have to create a counter pulse train task that uses a start trigger. The frequency of the pulse train should match the frequency of the AO sample clock on the 4461. To correct for the filter delay of the 4461, you'll have to calculate the length of time of the filter delay and specify this value as the initial delay for the counter pulse train. The output of the counter is then used to clock both AO and digital tasks on the 6289. The start trigger for the counter task will come from the 4461. So the sequence of events is as follows: 1.) Start the counter, digital, and AO tasks on the 6289, 2.) Start the AO task on the 4461, 3.) The start trigger from the 4461 gets routed to the counter on the 6289, 4.) The counter waits for the initial delay to pass before outputting the pulse train, 5.) The counter starts outputting a pulse train of the same frequency as the sample clock on the 4461 for use by the AO and digital tasks, 6.) The signals on the I/O connector from all three tasks are now synchronized.
Let me know which approach you're leaning towards and I can futher clarify some things if you still have questions. By the way, what sort of application are you developing? I don't typically see this mixture of devices and I/O types.