Since NI-9361 only supports a single task, you need to add all the counters to the same task.
You can create DAQmx Task with two channels as shown below. Create New NI-DAQmx TAsk...>> Acquire Signals>>Counter Input >>Period
(The Measurement Type)>>cDAQ1Mod1
(The Module Number) >>ctr0
(The Counter Number)
You can add new channel to the same task for the pulse width
Now you can use this single task to access both channels in LabVIEW as shown below.