Sal:
I can think of a couple options for your application. 1) Use internal timebase for both devices, but use start trigger to start the operation.
2) Use two external counters to generate 2 MHz and 1 MHz signal, since the counters will be using the same onboard timebase, your 2 MHz and 1 Mhz signal will be in phase and synchronized with each other. Use these signals to clock the pattern I/O operation.
3) If you are using PXI 6534 devices, they have onboard phase lock loop circuit, this means that they will be phase locked to the PXI backplane clock. You will need to start both devices with start trigger, and the two internal timebase should be in phase.
June