Add pictures to Photos.app
By default Photos copies everything into its own library on import. You can disable this in Preferences->General



Pictures which are not kept within the library itself won't be available in iCloud though (which may or may not be a problem for you).

If you want to use iCloud (e.g. for sharing of pictures between iPhone and Mac) you can keep the option selected and import the pictures into the library in batches. You could then also decide to keep the originals in the iCloud library only, and just have Photos automatically download hires pictures on demand. Settings for this are in the iCloud tab of Photos' preferences.