Can you post your sample code? Meanwhile...
1. If your "input" and your "output" tasks refer to ANALOG in/out, then you should be able to set up your sample rates & # of samples using the DAQmx Timing vi. You shouldn't need to use the on-board counters. (The rules may be different for Digital I/O -- I've done very little with timed DIO).
2. The "resources reserved" error is probably because you've set up a finite pulse train on one of the counters. Behind the scenes, DAQmx uses the board's other counter to implement the finite pulse train.
As a test, set up the counters for continuous pulse trains and you should see that you can generate two independent clock rates. It's even possible to have the faster one drive the slower one so that their rising edges are in sync.
Hope this helps you get started. Post back with a code sample or other questions...
-Kevin P.
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