sorry, title isnt descriptive, i couldnt make this short enough for a title.
also I dont know if the solution is in PHP or CSS so im posting in both places.

ok, so i have 4 files:

* index.php
* indexs.css
* template.php
* templates.css

in index.php i have:
<?php
include 'template.php';
?>

that works so now my page has a template (this same template file is being used for all pages) but now in index.php i want to add seperate content but no matter what i do it just shows up below the template.php and not in the area on the template that i want to have it in,, and i dont want to use position: absolute in the css.

No idea.. have to see ALL the code to know what's going on there.

but no matter what i do it just shows up below the template.php and not in the area on the template

As it will UNLESS you put your content INTO the template areas OR have variables in the template that insert the content data.

It's actually a PHP issue.