If I add a few more ROMs to my USB drive and plug it in, is it going to copy the entire collection again? If so, does it overwrite the files or keep them all? I am using a pi-3 with the latest version of RetroPie.
Only the files that do not exist on the RetroPie will copy over.
If the file located on our USB drive is
...roms/nes/Adventure Island.nes but the file
...roms/nes/Adventure Island.nes already exists on our RetroPie, it will not copy it and it will not be overwritten.
If, however, you change the filename to
...roms/nes/Adventure Island (USA).nes RetroPie will copy it, and you will have both, simply because the filename is different.
This is the default behavior, and the most logical.