Caveat: I haven't looked at LadyAda's instructions.
The directories are /usr/local/... (note leading "/" - it's important). The install process should create them if they are not there. I had already populated /usr/local before avrdude, so I don't know how avrdude's install will react if it isn't there. It's conveivable you need to do a "sudo mkdir /usr/local" before the "sudo make install" step.
In general, unix open source packages are built from source by extracting the source tarball, cd-ing into that directory, and issuing the commands
sudo make install
If you own the target install directories and there is no suid funny stuff, that last one can be just "make install" without the sudo.
As best I recall, avrdude only depended on libusb (to get support for my avrispmkII).
hope these random thoughts help...