If you're adding by card number, just enter each number once. Then, once you click the "Check" button, you will be taken to a page that shows "1" in the Quantity textboxes for each card number you entered. For any card that you have more than one of, change the number in the textbox next to that card number, then click the Add button.
Alternately, if you don't have that many copies but you have a lot of cards with duplicates, you can run through your stack one time for each copy. and add them in sequence using multiple "adds". I tried that when I entered my inventory, but found just changing the quantity as described above was more efficient.
-- Dan --
Note: Please see my profile for more info regarding trading (section updated 3/4/2024). I have added a large portion of my inventory to the site, and currently have trading turned on (details are in my profile).