Hi,
I scoured through the manual and found this on page 3-9:
The timebase for counter 0 uses a 1 MHz clock generated from an onboard oscillator. You must externally supply the timebases for 1 and 2 through the 50-pin I/O connector.
Having said that, what you might try is to generate a signal from counter 0 based on the internal timebase and then manually wiring that signal to counters 1 and 2 as a common source.
Hope this gets you going!
John N