To create my site, I have a local folder structure like this:

site
--images
----seriesA
----seriesB
----seriesC
1.jpg
2.jpg
scriptC.html

So my images are in different folders, all named 1....n.jpg. The script files are image galleries. They referenc the images by name. Since 1.jpg appears several times, I need the "seriesA/B/C" folders.

Now if I publish, everything is messed up. I want to tell Sitespinner to just leave my folder structure alone and upload it as it is! I can't put all files in one folder with all the scripts.
How can I do this? I appreciate your help.

The default publishing method is to "gather" all files and place them in predetermined folders. You can stop this action by disabling the "gather" function. This can be found in the Publisher window on the Pages tab in the Path Options section. Change the publishing method to use either relative or absolute links to the files. But be aware that you are responsible to ensure the links are correct; there is no way for SS to validate the links since it does not create them during publishing.