Hi snidjer and all-
Kevin is correct- the "User-Defined Signals" BNC connectors are referenced to DGND and will work well for your counter output. You will need to wire (via the spring terminals) CTR1OUT to USER 1 in order to route this signal appropriately.
In order to generate your two out of phase pulse trains you will need to consider the following: E Series devices do not support this functionality directly for pulse trains. One method to accomplish this is to generate a pulse train on one counter and then generate single pulses on the second counter with initial delays to be triggered by the pulse train on the first counter.
This will be particularly easy with your BNC-2110 because you can wire your CTR1OUT directly to a trigger line (in addition to the user-specified line) via the spring terminals. This means you will want to generate your pulse train on CTR1 and the triggered pulse on CTR0.
So the final step will be to determine the appropriate values for 'initial delay,' 'high time,' and 'low time' in a single pulse generation example. The initial delay be the origin of the phase shift between your signals. The high time will need to coincide with an appropriate pulse width in the pulse train at frequency (i.e. high time = period/2). The low time should be the remaining time in one cycle of the pulse train on CTR1 so that the generation on CTR0 will be complete in time for the next rising edge of the original pulse train.
Please let us know if you have any additional questions-
Tom W
National Instruments