either the captions are on or the thumb dots are on but never both
By default, the caption area is positioned on the image overlay (captionPosition="OVERLAY") and the default behavior for the overlay is to appear when the user hovers over the gallery and disappear when the user hovers out of the gallery.
If you want the overlay to be displayed at all times, you can set showImageOverlay="ALWAYS" (in JuiceboxBuilder-Pro's 'Customize -> Main Image' section). You could also choose to set showInfoButton="TRUE" ('Customize -> Button Bar'). This overrides the default behavior of the overlay and allows the user to toggle the overlay on and off via the Info Button on the Button Bar.
Alternatively, you could position the captions somewhere other than on the overlay (for example BELOW_IMAGE, BOTTOM or BELOW_THUMBS) where they will always be displayed (except for during image transitions when they fade out and back in again).
Ideally, I would have the thumbs below and a caption to the right; is this even possible?
This layout would not be possible. You can certainly position the thumb dots below the main image (using thumbDots="TRUE" and thumbsPosition="BOTTOM") but it is not possible to position the caption area to the right of the main image. The caption area can be positioned using the captionPosition configuration option, whose possible values are OVERLAY, OVERLAY_IMAGE, BELOW_IMAGE, BOTTOM, BELOW_THUMBS and NONE.
For short descriptions of each of these possible values, please see the the captionPosition entry in the Config Options page.
If it's not, it ought to be.
If you would like to make any suggestions for future versions of Juicebox, please post then in the Feature Requests thread.
It keeps them all together and ensures that they are not overlooked. Thank you.