By default the counter tasks will use the built-in 100 MHz timebase of the DAQ card (or possibly one of the slower timebases that's derived by dividing down the 100 MHz one.) You probably don't need to specify a timebase explicitly for your usage in generating pulse trains. Look at the shipping examples for pulse train generation and you'll see that those don't specify a timebase either and they work just fine.
To sync up 3 pulse trains, they should be configured for a start trigger from a signal you can control so that you can be sure all tasks are started before you assert the trigger. Often this can be on of the DO lines that also has a PFI designation for use by the counters. It sounds like you'll also need to make use of the 'initial delay' setting that the shipping examples (unfortunately) do not illustrate.
-Kevin P
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