I am using the following method on a rooted NC and using either Aldiko or Overdrive Media Console with no probs whatsoever. I use these because I like to read my epubs in landscape mode and for some totally inexplicable reason the BN reader can't do this!

You must have Astro File Manager installed (free in the Market). Astro allows you to add new file extensions by the following preferences:

Astro settings>Data>Edit File Extensions>New

Extension Name: epub (no period)
MIME Type: application
Subtype: epub

Then Save

Now when you double-click on the ebook file it will ask for whatever reading program you want to use to read, i.e., the reading app that is on your Nook Color. If you have Desktop Visualizer installed (also free in the Market) you can even make a shortcut for your book on your [rooted] Home Screen, e.g., I am using Zeam launcher for my home screen.