Unfortunately you won't be able to work on Magento without knowing at least some PHP so I would recommend that you at least learn the basics of the language (including how to use classes).
If you are intending to focus on just styling of the page (no new functionality that would require some code changes) then you should look at how magento layouts and themes work. All the content can be found in app/design
folder and this is the place where the least PHP can be found.
Layout files define (if not otherwise speccified in code) which blocks, css and javascript files will be added where (this is the place where your javascript inclusion should go).
Templates are the actual block HTML content files (it is there where most of HTML is written and dynamicaly changed with PHP).
Note that layout and template files can be overwritten by placing them on different locations so you should never rewrite default layout and template files.
Resources
The best resource would be to look into already existing default layout and template files.
Google :)
Stack Overflow - This link is on how to add your own JS file to theme
Alan Storm tutorials - They are more technical so you should learn basic PHP first (he also wrote a book that extensively covers the Magento layout system but requires you to know PHP).
Magento For Designers - I didn't read the tutorials but they seem to go through Magento without expecting too much PHP knowledge