I am creating a HTML online Manual and storing the pages in SharePoint and using SharePoint Designer. I want to create a panel either on the top or the side, so that when the user scrolls down the page, the table of contents or links to the pages is on the side. What or how do I do this?
This isn't a SharePoint-specific question. It is more of a generic HTML question. However, here are some ideas for you:
1) Super old school way: HTML Frames - http://www.w3.org/TR/html4/present/frames.html. This is basically where you use frames on a page to show content from other HTML pages in "frames". Used a lot in old school websites to TOC type content. This is a simple way to use a single TOC HTML file.
2) Newer school way: use a fixed position DIV for the TOC so that the content of that DIV stays in the same place no matter how far down you scroll.
Now for a SharePoint way:
3) Use Wiki pages. In SharePoint wiki pages you can use reusable content to share a TOC among multiple Wiki pages. Here is a pretty good TechNet article introducing SharePoint wikis: http://technet.microsoft.com/en-us/magazine/2007.01.wiki.aspx