Jalbum currently has no user interface for setting folder names for the "thumbs" and "slides" folders, but with three lines of code in the file system/init.bsh you can change this. Do like this:

• Open the file system/init.bsh under Jalbum's installation folder for editing. You can use Jalbum's internal text editor if you wish (CTRL+E). You can press CTRL+ALT+P to open Jalbum's installation directory, then navigate to the system folder. Now drag and drop the "init.bsh" file onto the editor window.
• Add the following code to the end of the init.bsh file:

  setAccessibility(true);
  engine.thumbDirectory = "smallimages";
  engine.slideDirectory = "closeups";
  

• Save your changes. Now make an album.

This trick should work with most skins, but there might be some that assume thumbnail images to reside in the "thumbs" folder for instance. In such cases, tell the skin developer to use the getSlideDirectory() and getThumbnailDirectory() of the engine instead of hardcoded names.