For reference, the Search Engine Optimization support section can be found here.

When you create a gallery with JuiceboxBuilder-Pro, select the 'Add SEO Content' checkbox in the 'Customize -> Sharing' section and SEO code will be generated. The SEO code will be included in the gallery's 'index.html' file (which can be used to view the gallery on a page of its own) but it will also be presented in the 'Get Embed Code' window on JuiceboxBuilder-Pro's 'Publish' tab. As long as you follow the regular embedding instructions here you can just copy and paste the entire embedding code into your web page and all should be fine.

However, things are complicated slightly with your own setup. Not only do you use a baseUrl (which would mean that you would need to modify the paths to the images in the SEO code as JuiceboxBuilder-Pro has no knowledge of your custom gallery structure when generating the SEO code) but you also switch between multiple galleries on the same page. You would probably need to merge the SEO code from your multiple galleries (making sure that the paths to the images are correct for each gallery) and manually insert it into your web page (inside the 'juicebox-container' <div> within <noscript> ... </noscript> tags, which is how JuiceboxBuilder-Pro presents the SEO code).

Try creating a sample gallery with JuiceboxBuilder-Pro (with the 'Add SEO Content' checkbox selected) and check the 'Get Embed Code' window on the 'Publish' tab to see the format that JuiceboxBuilder-Pro uses for the SEO code if you plan to implement it manually for your own web page.

Placing the SEO code (<img> tags) inside <noscript> ... </noscript> tags is not hiding the images (so Google should not penalize your site for this). It is simply telling the browser that this is what should be displayed if JavaScript is disabled. Not only is this a method of adding the SEO code to your web page, it also ensures that your gallery images will still be seen even if JavaScript is disabled in the browser.