When you see a mistake on one of your pages, you can simply login on this page by adding ?login or &login to the url in the address-bar in the browser:
In addition you can even use your username in the url:
Hint: Save your link as a bookmark, so you only have to type in your password and can start editing your site
In your particular template you can file your javascript- and stylesheet-files in the js and css folders, more is not necessary. The cms uses these files, when the content is shown.
For an easy development of own modules or other great javascript functionalities, there are all popular javascript libraries as modules for pinion available.