Ordinarily, if you want to have 1,000 different galleries on your web site, then you will have 1,000 gallery folders to deal with.
You could have all your images stored in a single folder on your server (as you currently do) but you would need to manually adjust the paths to the images in the gallery configuration files as JuiceboxBuilder would have no knowledge of the fact that you want to store your images in a custom location when you create your galleries.
Even using a global search and replace action in a capable text editor, this would take some time to do for 1,000 galleries.
It would be easier to keep each gallery in its own folder. It helps to keeps things organized on your server and you can just swap out an entire gallery folder if you want to update a gallery in the future.
Perhaps the most efficient way to do what you are looking to achieve would be to use a Flickr account as your source of images and tag your images accordingly.
Each gallery could then be configured to display only certain tagged images (using the flickrUserName and flickrTags options).
You should be able to tag images in bulk on Flickr so it might not take too long to set up.
You can then have all your galleries share a single 'jbcore' folder (rather than having one per gallery) to minimize the upload.
This has the added advantage that when a new version of Juicebox is released, you need to update just a single 'jbcore' folder on your server (rather than 1,000). Please see the Using an External jbcore Folder support section for details.
You can simplify things further by having all your galleries share a single dummy configuration file.
All galleries need to have a 'config.xml' file (even if its content is not used) but you could upload just one for all your galleries to share (all galleries would point towards the same 'config.xml' file via the configUrl option) and you could set all your configuration options in the embedding code (in your HTML pages). Please see the Setting Config Options section.
Now, with your images hosted and tagged on Flickr and with a single 'jbcore' folder and 'config.xml' file on your server, all you would need for each galley is unique embedding code in its HTML page.
For example, the embedding code for one gallery might look something like this:
<!--START JUICEBOX EMBED-->
<script src="path_to_shared_jbcore_folder/jbcore/juicebox.js"></script>
<script>
new juicebox({
containerId: "juicebox-container",
galleryWidth: "100%",
galleryHeight: "600",
backgroundColor: "#222222",
configUrl: "path_to_shared_configuration_file/config.xml",
useFlickr: "TRUE",
flickrUserName: "your_flickr_username",
flickrTags: "iris_number_seven"
});
</script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->Alternatively, you could maybe have just one gallery and have its content change dynamically.
You could perhaps have a drop-down menu of all your iris varieties. When a user selects one, you could run a JavaScript function to load or reload the gallery with the chosen subject (setting the flickrTags option dynamically).
Take a look at this Lite Flickr demo gallery to see something similar in action. You can view the source of the web page in a browser and copy or modify the code to suit your own needs.
(The demo has a text box to allow any Flickr tags to be entered but, as your scenario has a known collection of tags, you could present the user with a drop-down list of existing tags to choose from.)
If 1,000 items in a drop down list is too many, then you could maybe have a few subheadings and split the idea into a few galleries (each with 100 or so drop-down entries).
When an iris variety is selected, the JavaScript function could do more that just reload a gallery if you wanted it to.
It could change or display other content on the web page. You could maybe have a synopsis of the chosen iris variety below the gallery which could change when the gallery is reloaded. Knowledge of JavaScript would be required but it could prove to be quite a powerful solution.
I hope this gives you some food for thought.