Here's (probably) the easiest way to do it:

(1) Copy your gallery folder.
(2) Open one of the gallery folders in JuiceboxBuilder-Pro (see here for details).
(3) On the 'Images' panel, delete the images that you don't want in your first gallery. You can select an image with a single left-click and you can also Ctrl+Click a selection of images or Shift-Click a block of images. You can then delete the images(s) via Crtl+D or 'Images -> Delete' from the drop-down menu at the top.
(4) Re-save the gallery on the 'Publish' panel.

Now repeat the process with the other gallery folder and delete the images you don't want in your second gallery.

(Incidentally, you can do this manually by editing the gallery's 'config.xml' file in a plain text editor and manually removing <image> tags (and then deleting the corresponding images and thumbnails from the 'images' and 'thumbs' folders) but using JuiceboxBiulder-Pro to automate the process is easier.)

You might want to keep a copy of your complete original gallery as if you delete an image, you'll lose the image's caption and if you decide to re-add the image to the gallery at a later date, you'll need to manually re-add it's caption, too.

Also, I don't know if you already do this but you might like to embed your captions within your images as IPTC metadata.
That way, the caption text will become part of the image file itself and wherever the image goes, the caption goes too.
JuiceboxBuilder-Pro has the ability to extract the IPTC Document Title as the image title and the IPTC Description as the image caption (so image titles and captions can quickly be set without any manual entry) via the 'Images -> Titles -> Use IPTC Title' and 'Images -> Captions -> Use IPTC Caption' options from the drop-down menu at the top.
You can add IPTC data to images (multiple images at once) in imaging programs such as Adobe Lightroom and Photoshop.
Please note that when instructing JuiceboxBuilder-Pro to extract IPTC metadata, all image captions are processed at once (it is not possible to extract IPTC metadata on an image-by-image-basis).

I hope this helps.