There are several things that need to be specified here. I'll answer the last 3 questions, then go into a little more detail.
1) How to measure the two speeds?
Your MIO board contains two counter/timers, 0 and 1, which can be internally or externally clocked to 20 MHz. You can use the Measure Period VI, or count pulses VI, and configure and check each counter individually. I think that counting the number of pulses during a specific amount of time works the best. You specify which counter by wiring a 0 or 1 to the counter input. Configuring or running one counter has no effect on the other.
2) How to understand selecting the various counters?
As stated, there are only two, 0 and 1. The only designation you need in your code is to wire a 0 or 1 whenever th
e input "counter" is encountered.
3) Does this interfere with other data acquisition?
No. Analog output, analog input, and counter/timers all have separate hardware on the board, and are not effected by each other.
*Notes*
Different PFI lines can be used for counters. PFI, or Programmable Function Input, are lines that can be programmed to go to different signals as inputs, but have a defined output signal when configured as output.
Therefore, you can tell counter 1 to use PFI7 as its gate signal, rather than the default PFI4. (PFI4 defaults to counter 1's gate, but can be configured for something else). I don't see a reason why you'd need to do this, but there are examples (and I had one).
i.e. You have several signals in which you'd like to read the frequency, but the readings don't have to be high speed. You could put all the frequencies on the PFI lines, and then set the counter gate to PFI1, do a reading...then switch to PFI2, and do a reading....
Let me know if you n
eed more details.
Mark