uploading external files

hello
i am new to the wordpress.org platform and have this preloaded with a host provider and i am using the platform to create a website.
i have created a navigation bar and have the following to upload to my site
3 image gif files
and a java script file
aswell as the php file with the script link in the head tag JavaScript1.2
and the script code in the body tag
i need to know where in the root directory of my site do i need to upload the javascript file aswell as the releavant gif files
i then need to get the script code into my template files
if any one can help with that ide be a happy bunny
then all ill need to do is find out how to add the relevant page links to the code
hopefuly someone nice and clever can answer this for me as ive had no luck working out how to use the navigation bar plugins