I'm not clear on what exactly you want to do in terms of generating a PWM signal as an input to the 7344. The 7344 can produce a PWM signal, which is independent of the onboard PID loop. The 7344 uses a 10.240 MHz clock and divides it down to produce the PWM signal. You can select certain frequencies for the PWM which correspond to the divided down 10.240 MHz signal. The PCLK (or Pulse Clock) line can also be used to input your own clock which is divided down by 256 or 32,768 depending on what you select in software. If you were using the external PCLK at 256, then a duty cycle of 50% would be high for 128 pulses followed by low for 128 pulses. You can check the Flexmotion Software Reference Manual or the Flexmotion LabVIEW help for detail on setting the parameters.
Regards,
JR A.
Application Engineer
National Instruments