You can SSH them into the file system, but if you copy them into the stock photos folders, they won't show up in the camera roll or folders through the Photos app. This is because they have to be assigned a random file name and doing it with that method doesn't achieve that type of cataloging. Instead, it just retains the original file name. Although they'll be accessible through iFile, they won't be accessible through the Photos app so you won't be able to set them as a wallpaper with the stock method (if they are copied to the device via SSH).
One alternative would be to create a theme with a wallpaper. You could then change the wallpaper through iFile rather than with the stock method and you would be able to set any of the wallpapers you transferred via SSH.