I do want to keep Airport Utility 6.x - so can I rename the main or basic part of an OSX program just like I would a file and have things work normally? If the answer to that is No, how about sticking the 5.6 version in a different location?

On many applications, that's not an issue. I have multiple copies of Office, Turbo Tax, BBEdit, Stuffit Expander, VLC, Mac the Ripper, OmniWeb, and GraphicsConverter. Many are just renamed, though some are in their own folders (folder's renamed, application with it's original name).

For me, it depends on if there are other things in an app folder for it.

But the other problem is if it uses files from other locations, like photoshop using plugins. I could see an Apple app, like the Airport Utility, using some plugin or extension saved somewhere else, that would get updated or replaced when you install the new one.

Most likely it is fine. I suppose the best way to try it out is to make a backup of your whole system, then duplicate the app and rename one of them. Install the new one, which will likely overwrite or delete the one you didn't rename. And then try out the old one.

Aaron