I want to make a website in two languages. I've looked around and settled on the directory option of separating both languages. How do I make it work?

Let's say I have the following three files for the landing homepage, the English page and the Spanish page:

http://www.domain.com/index.html
http://www.domain.com/en/index.html
http://www.domain.com/es/index.html

Let's also say that /index.html will be in English, with a link to /es/index.html. In turn, /es/index.html will have a link to the English version. Would this be back to /index.html or to /en/index.html. How do I get both English versions (the one at the root and the one in the directory) to actually be the same file in the same directory?

I'm new to this, so I'm not using any scripts yet. To me, the obvious solution is to duplicate both English versions and have the one at the root point to files under the /en/ directory, but I'm not a fan of duplication and I've learned that search engines really frown upon that. Anyone point me in the right direction?