Your questions are answered in the help of the VI (CTRL + H or Menu --> Help --> Show Context Help).
1) Source specifications : (text from the help)
Optional controls are located on the left side of the front panel. You will have to use your scroll bar to reach these.
You cannot use the digital I/O lines. See the user manual of the card for the corresponding pins of the PFI lines.
2) Gate : (text from the help)
The counter increments its count everytime a pulse comes into its source input, and transfers that value to memory upon every time a rising edge comes into its gate input.
The Gate specification control allows you to change this. (other pin, falling edge...)