When uploading photos, is there a way to only copy new ones?

Assuming you are using the ViewNX2 software that came with your camera... Go to the Options area and select the Preferences tab. There will be a checkbox that states "Transfer new files only". Make sure you select this, and you should be good to go.

If you are using a different software to transfer photos to your computer, then the procedures will be different, but look for a similar setting in the software you are using.

If you would like to use Nikon's ViewNX 2 software that came with your camera but misplaced the CD, then you can download the software from here: ViewNX 2 Download.