Website integration with Permalink problem

Hi, I am using WP 2.6.3

I already have a website driven by template for the top bar that includes drop down menus for navigation and external CSS for controlling the design. I want to add WP to my website. I tried to things that worked for me so far but only using the “UGLY” links like ?p=10 while I want to get /year/month/day/post

I tried those two:
1. I modified the header.php for WP to include all code including javascripts but it was pain to do so.
2. I kept my index.php but in the mainContent div I put
<?php include(“index-wp.php”); ?>

This was much much easier than the previous method.

The problem starts when activating Permalink. I am using mod_rewrite.so in Apache. The main website still looks ok but once you click on a post I lose my CSS and javascripting. The reason is I am using relative linking for css and .js files
I tried to solve this issue by including two lines for every css .js but with different locations for ex: “css/main.css” and “../../../css.main.css”
It worked but I found out that now all my top bar links for main website are trying to load from new location.
For ex: website/year/month/day/post/tour.php instead of just website/tour.php

Can someone direct me on what I need to do in order to fix this problem? [I am a designer not a scripter]

Thanks