If you have structure like this
then on index.aspx if you want to add the link to js and css
you can add like
<link rel="stylesheet" type="text/css" href="css/style.css" />
And if you want to add on page2.aspx
you can add like this
<link rel="stylesheet" type="text/css" href="../css/style.css" />
Same will go fr js. You can fix the links and i think it will work for you. If you are having anyother issue other than this you must provide the code here for better understanding.