When I "publish", chosing the webfolder, JB overwrites the existing "image" folder,- how to avoid this?
This cannot be avoided and is by design. It ensures that the 'images' folder is always up-to-date and contains the correct images for the gallery (for example if images are added or removed from a gallery or if images are resized or if a watermark is added or removed).
There is already an "index.htm" in the root structure,- so both the original index.htm and the JB should be in the root???
If you have existing files on your web site that have the same filenames as those in your gallery, then I would recommend embedding your gallery using the baseUrl method as documented here.
It allows you to keep your gallery as a self-contained entity with all the gallery files stored inside the gallery folder.
You would then upload the complete gallery folder to your web server (rather than just the contents), thereby avoiding the chance of any filename conflicts.
And the image folder: are the JP images supposed to sit inside the existing image folder?
Just upload your complete gallery folder (not just the contents) exactly as it has been generated by JuiceboxBuilder-Pro and follow the baseUrl embedding instructions.