javascript and template division

[eluser]mysterious[/eluser]
I am developing an application with codigniter. I have divided my template into 5 files.

meta.php, header.php, maincontents.php, sidenavigation.php, footer.php

is this division right? Where do I write my javascript or jquery functions as different controllers has different functions and these functions include different jquery plugins.
If i write my scripts in meta.php then every page will load that script, that i think is a bad thing.

confused !!