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How do you generate 3 independant Counter O/P Frequencies

I would like to generate 3 counter TTL signals (each with variable frequency, duty cycle and initial phase lag from the first counter). I have 2 PXI-6133 cards each with its own BNC2110. So I'd be using Counter 0 and 1 on one PXI-6133 and Counter 0 on the other. I want to be able to start and stop each counter seperately. Is that possible? I've tried integrating all the example Counter Output vi's in the Example Finder, but that doesn't seem to work for me. Frequencies required are up to 50Hz. Also, while I am controlling devices (valves) with the counters, I shall be running another vi that reads Analog Input (pressure readings) - 8 on one BNC2110 and 2 on the other, with sample freq of 100kHz for 1M samples. Should I be worried that the system may slow down and change timings of the counter?
I would appreciate any help offered. Thank you.
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