Ok, I am almost there now. Here is what I found.

I was editing the section of debian/rules that dealt with configure. Further down there is a section for install: build "# Add here commands to install the package into debian/appname." When I edited the prefix being passed in there to include debian/appname/prefix/usr" I got it for the most part.

However, in the deb are a few files that are still outside the prefix. copyright, changelog.gz, README.Debian, changelog.Debian.gz.

Any idea how I can keep those in the prefix?

Thanks so much for the help!