Ok, first step.
In DAQ assistant, set up an input (in this case, since you have no counter I would say analog input). Then set the input to read off of ai0 (or whichever you want, you can pick arbitarily). Then at the bottom of the Assistant, you should see a tab labeled "Connection Diagram" clicking there will tell you where to wire the + and the - sides of your signal (but remember, it is analog now, not digital).
That should solve one of your problems.
The other problem is a little more complex, and in reality has a ton of different solutions. I think your best shot is to use the express vi for spectral measurements.
Found in Express -> Signal Analysis -> Spectral
This is a bit like like putting out a match with a fire hose (way more powerful than what you need). But parsing out that information will give you what you want (namely, the frequency component with the highest magnitude). There are a ton of other spectral measurements that you can do to get this same information. If this is beyond the scope of your project, and you foresee doing lots of this type of measurement, you should probably look in to getting a board with more counters.
Best of luck,
~milq
