Hi,
There will be no conflict ressources if you generate continuous pulse train on 2 counters and operate an analog acquisition on other channels. But remember that "This is a question linked to the internal circuitry on the board. You are not allowed to have more than one task running (simultaneously) of the same type (like Analog input) because the internal circuitry is already reserved. The only way you will be able to do this is to add both channels you need to the one Analog Input task and read/write to the channel of interest at that point in the code. As you found out, digital is not in the same circuity, so it is allowed to be in a different task running simultaneously".
Besides, do not try to generate FINITE pulse train on 2 counters because you will get a ressources conflict : I mean, finite pulse train already uses 2 counters (one to generate and the other as a gate).
To help you about retrigger, look at the "Gen dig pulse-retriggerable.vi" located in Help/Hardware Input&Output/DAQmx/Generating digital pulse.
Finally, it is easier to use internal clock whereas signal coming from a counter as a clock.
Regards
David D.
AE - NI France