Install WordPress in a subdirectory on GoDaddy main domain

Hello,
I have searched a lot, and I know there are a lot of articles concerning the following, but I didn’t find anything. I guess I’m searching in the wrong way :S.

This is my situation; I want to host two different sites on one godaddy account. I have two domains and have the account that allows me to host multiple sites on one hosting. This is where it gets ugly, I wanted to separate the installation of WordPress into two subdirectories. But by default when installing WordPress on the main domain, godaddy adds the files directly on the root. Even if I put a subdirectory in the settings of the godaddy installation, the site then can be accessed by example.com/file and not example.com.

So this is what I did, after installing WordPress on the root, because I don’t want to access the site by entering example.com/file. I moved the root install to its own directory, using the following article: http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory. It worked fine, until we noticed that images/content being uploaded, are being sent to the root, and not the designated subdirectory. Also godaddy did an automatic update and added all the files to the root.

Is there another way to install WordPress in a subdirectory and using the main domain, on godaddy? Or what I did above was the right way?

Thank you,