Jordan,
"Your device" is the device to which you are connecting the DAQPad. The "counter" is actually the counter on your DAQPad. You shouldn't worry about using an external timebase - you don't need to wire anything to the source if you specify "internal timebase."
If you are using counter 0, the output should appear on pin 2, or pin 40 for counter 1. You can change this pin through the use of the "Route Signal" VI on the Calibration and Confidguration Palette.
Hope this helps,
Ryan Verret
Product Marketing Engineer
Signal Generators
National Instruments