Hey oracle 765,
So I checked out the source code. First of all, it's strange that you have some code before your header (the html and head tags). The doctype and all that up until the body tag should all come first, then insert your footer and top menu codes. All you need to do to put your side menus into include php files is to replace them with the php code e.g. <?php include ("rightmenu.php"); ?> at the exact place where it is now on the page and it will display the same since php is merely replacing that with the content of your rightmenu.php file. All you paste into that one is the code from the <div> where your menu starts to is respective closing </div> tag. Nothing else.
About your overlapping question, you can cut out the overflow of an element in your css styling by setting overflow:hidden; in your parameters.
About your picture and text, either you can cut out the overflow of text, or you can set the element you want on top with a higher z-index value. By default, all elements have z-index value set to 0. You can prioritize an element and put it on top by setting it to e.g. z-index := 10 in your css code.
Hope that helps.
Epsilon