You can create Juicebox-Pro galleries directly within the Showkase interface.
Please see the Getting Started support section for details.
However, you could also create your galleries with JuiceboxBuilder-Pro and import them into your Showkase site using Showkase's 'Site -> Import' functionality.
Here is the procedure:
(1) Create a Juicebox gallery on your computer with JuiceboxBuilder or the Lightroom plugin.
(2) Upload the complete gallery folder (not just its contents) to your web server using an FTP program (such as Filezilla). (I recommend uploading it to a location outside your Showkase directory if possible, just to keep things separate from each other.)
(3) Go to 'Site -> Import' in your Showkase site.
(4) For the 'Import path', enter the path to the directory containing the gallery folder (not the gallery folder itself) with a leading slash '/' to denote your root directory.
(5) Click 'Scan' and select the checkbox (in the 'Import' column) next to the gallery folder (or folders - you can import several galleries at once if they are all in the same parent directory) that you'd like to import.
(6) Click 'Import' and 'Publish'.
Once a gallery has been imported, it becomes a genuine Showkase page (just as if the gallery had been created in Showkase itself) and it can be edited from within the Showkase interface if necessary.
You can upload the gallery folder to anywhere you like on your web server as long as the import path is correct.
For convenience, I'd recommend just uploading the gallery folder to your root directory. You would then just use a single slash '/' as your import path.
Incidentally, after importing a gallery, it is safe to delete the original gallery folder that you uploaded for import as Showkase will have copied all the gallery files across to the Showkase site. (Showkase does not automatically delete the gallery folder as it may be part of a different active site.)
I hope this helps.