Thank you for the link to your website.
I see that your website is essentially a single page site (as far as a visitor to your site is concerned).
The browser never leaves the main page and a selected gallery page is loaded into a frame on demand.
If possible, I would recommend embedding a gallery directly into a web page rather than using a frame (or an iframe) as there are certain drawbacks to using frames (such as the inability to expand a gallery to fill the browser window). Please see 2) Using an iframe for details.
I'm not sure that there's going to be a quick and easy way to convert all your current galleries to Juicebox ones.
There are no similarities between the structure of your current galleries and Juicebox galleries and there is no direct migration path.
There is an added complication that your current gallery pages also include information about the selected iris variety so you wouldn't be able to just swap your existing gallery pages for Juicebox ones (unless you intend to incorporate all the text into your Juicebox galleries as image captions).
I'm not quite sure what I would do if I were in your position. Whatever you do, I think you'll probably have a good deal of work ahead.
I might try to incorporate the text accompanying each gallery into the gallery itself as an image caption.
I might then use JavaScript code to load the selected gallery into a container on your main page, replacing the frame.
This brings us to the structure of your galleries and site.
If you are creating all your Galleries with JuiceboxBuilder-Pro, then it would be easier to just leave all the galleries in their folders and upload the all the folders to your web server. There would be no need to change any paths in the 'config.xml' files and editing or updating galleries would be a very easy process.
You could then load the galleries into your main page using the baseUrl switching method. Please see 'Switching between Multiple Galleries using JavaScript' in the Embedding Multiple Galleries support section for details.
If you really want to keep all your images in a single folder, then editing all the 'config.xml' files does not need to be a time consuming task.
With a text editor such as Notepad++, you can edit multiple files at once so you could open all your 'config.xml' files in the editor and a search and replace action could be applied to them all. As all your images (and thumbnails) are all in the same folder, the path to the images (the prefix you would have to add to all your imageURL and thumbUrl entries) would be the same so editing all your files should be quite quick and easy with just a couple of search and replace actions.
However, I'm not sure there would be any advantage to leaving all the images in your 'irises' folder and there would certainly be benefits to using the default gallery structure (no need to edit any files and easy to maintain individual galleries).
If you are looking for an automated solution to creating and listing multiple galleries, then you might be interested in another one of our products - Showkase.
Showkase is a PHP web application which allows you to create a complete portfolio web site (integrating multiple galleries) online.
Showkase has full support for Juicebox-Pro (and SimpleViewer-Pro) galleries and the galleries can be created within the application itself in a web browser interface (or created with JuiceboxBuilder and imported).
You can create Gallery Index pages and have as many galleries listed on each Gallery Index page as you wish.
Each gallery is represented by a thumbnail image with the gallery title displayed below and the gallery is opened when the user clicks on the image.
Demo sites created with Showkase can be found here and a sample Gallery Index page can be found here.
Showkase can also create non-gallery pages (About, Basic and Contact pages) where you can add information about yourself (or any other content you like).
All of this is done automatically within the Showkase interface without the need for any manual coding at all.
Showkase can be purchased as Showkase-Standard (which comes with Juicebox-Lite and SimpleViewer-Standard, the free versions) or Showkase-Pro (which comes with Juicebox-Pro and SimpleViewer-Pro).
The only difference between Showkase-Standard and Showkase-Pro is the bundled viewers.
However, Showkase does not have any built-in ability search functionality (like your current web site has) and you might find that listing a large number of galleries on each gallery index page is not an ideal solution for you.
I'm really just thinking out loud and letting you know of a few alternatives that you might like to consider.