Yes. All of your work is automatically saved in your original PowerPoint presentation. If you are using a read-only file, you must save it as a file that can have changes written to it, or else your changes will not be saved.
The information LecShare saves does not effect the way you edit or present your slide show in any way from within Microsoft PowerPoint.
LecShare Pro for Office 2008 on Mac stores all information in a separate file in the same folder as your .ppt/.pptx file. It will have the exact same name as your .ppt/.pptx file, plus it will have a ".lsp" extension added to it.