Since they are small and the WiFi is set up now, it doesn't take to long to transfer this way. In Cyberduck, click 'Open Connection' type in the local IP address of the Raspberry Pi where RetroPie is installed (usually 192.168.1.x, where x is another number), username of the Pi (default for RetroPie Image = pi), password (default = raspberry), and port (use port 22) open up a SFTP to allow me to transfer some N64 ROMs to the Pi. To do this, open Cyberduck on another computer where your ROM is located. I use Cyberduck, as you can open up the raspberry pi folder directly and drag and drop the ROM files into the proper folder. This is accomplished using SSH File Transfer Protocol (SFTP) which is just like using SSH to get into your pi (both use port:22) but it allows you to transfer files.
Once you do have your ROMS, they are usually pretty small files, and so are conveniently transferred to the Pi using WiFi.
