javascript and css links not working on sever

The proper way to include styles and scripts is with the wp_enqueue_script() and wp_enqueue_style() functions. The codex pages on both of these functions covers how to use them very well. Basically you just need to give the script the source (do it relative to your current PHP file) of the script/style and a slug to reference it by. If you’re enqueueing conditionally, then you should look at wp_register_script() and wp_register_style() as well.