Already installed Multisite w/ subdirectories on Godaddy

I am very new to multisite. This is my first install and I have apparently made a mess of it.

I have GoDaddy hosting which I see cannot be installed with subdirectories. However, because my site was 2 years old, I did not have the option of subdomains. So now the site is set up with subdomains.

What should my next step be in this situation? I would still like to be able to use multisite. Did I mess up the installation forever?

My goal for this installation was to link my website motorcitymuckraker.com to another website marijuanainthemitten.com so that we could pull content from the latter to the former. I'd also like to be able to give individual writers their own blogs so that content can appear on their blog, marijuanainthemitten.com and motorcitymuckraker.com.