there are good reasons to get as much of your javascript and css put into external files. these include
so what is the best way to add javascript, jquery, css in drupal? it is quite easy
drupal_add_js(drupal_get_path('theme', 'your_theme') . '/javascript/banner.js');
drupal_add_css(drupal_get_path('theme', 'your_theme') . '/css/main_menu.css');
Note, that while drupal_add_js and drupal_add_css calls work great in blocks and modules, they will not work directly on page.tpl.php pages.
you can increase your performance (on a production environment - i don't recommend for development) by going to
Administer >> Site configuration >> Performance or directly at
/admin/settings/performance
and setting
'caching mode' to 'normal',
'optimize css files' to 'enabled', and
'optimize javascript files' to 'enabled'
if you look at the source code you will notice css and js files with weird names such as
"9511e5f39a8980800595da73ff8ee7e0.js"
which is an optimized, combined file
if you test your website with an application such as yslow or pagespeed, you will see the improvement
back to drupal tips...