You are doing things the hard way, a very hard way.
(Layers is an old-fashioned term for a div, a generic container. You have hundreds of these when you really only need three or four.)
The three column layout idea simply
creates three divs and you stick each link into the appropriate div. It does not use the absolute
positioning that you do, which is a very bad way to do things. Because each link is in it's own personal little div with it's location sharply defined, if you try to move it, it goes to the same place every time, and thus it can sit over the top of another existing link. Most people
advise never to use absolute positioning of anything.
Also you are individually styling each link - set a style for the links once using css, and then they will all look the same. Overall you are going to a great deal of effort to do something straightforward.
Read up on external style sheets, where you
define the styles once in a single file, and then simply refer to that file on each page that you wish to use those styles. A css stylesheet can contain dozens of styles which you use as and when needed. But it is best to apply a set of general styles to the body - the whole page - and then you only need to add other styles that are specific to some part.
Your choice of background and colour makes the pages difficult to read. I strongly suggest dropping the background image to make things more readable.