When you upload images via the WordPress media window, the images in your WP-Juicebox gallery should initially be in the order in which they finished uploading.
To sort images after a gallery has been created:
(1) 'Edit' the post containing the gallery
(2) Click the 'Add Media' button
(3) Select the 'Insert Media -> Media LIbrary' section (selected by default)
(4) Choose 'Uploaded to this post' from the drop-down menu
(5) Drag and drop the images into your chosen order
(6) Close the 'Add Media' window
You may need to clear your browser's cache after reloading the gallery.
If the images initially look like they are in the right order in the media window but do not appear in this order in your WP-Juicebox gallery, just drag and drop a thumbnail into a new position and then drag it back. That should be all that is required to change the order from the 'finished uploading' order to the visible 'menu' order.