After working with the Addit! software a little more I've had better results.
First off it seems that the program works best if it is able to directly access a zipped file before I've had a chance to open it and purge some of the unneeded files like the readme's.
I'll take a downloaded (zipped) file and either put it on my desktop and drag the whole zip file to a temp folder or I guess I could just download the aircraft zip files right into the temp folder itself. From there as long as the file hasn't been unzipped the Addit! software seems to work very well at extracting and placing the appropriate files where they need to go.
I was able to add several more addons from this site last night with success.
One thing I have noticed is that there can be a tendency for the addon aircraft's folder to get loaded into the main FS9 folder and into the actual FS9 aircrafts folder as well.
Now to be absolutely fair to the Addit! folks I very well may have caused this by mesing around with the files prematurely but when I've uploaded new a/c and they haven't appeared in the aircraft list in the selection menu it has always been because the files have been duplicated, with one in the FS9 aircraft folder (where it should be) and one in the FS9 main folder (where it should not be).
So looks like I'm getting the aircraft addons to work. Next I'll start trying some of the other features like scenery addons, paint schemes and AI uploads.