I'd vote rather for a more generic phrasing. `/usr/share` should be right for most users as this is usually the path used by distro packages. `/usr/local/share` is the default if you compile from source yourself and do not specify an installation prefix, this is not the way *most* users do install Geany, I guess. Those users who install Geany from source and use a custom prefix, probably know what they are doing and so also can mentally replace the provided default path in the documentation/README with that they used for `./configure`.
In the documentation, we already have a few paragraphs about different config/resource file paths, see http://geany.org/manual/#configuration-file-paths. Maybe we could just refer to this part of the docs in the README?
Something like "$PREFIX" could rather increase confusion for users rather than solving it.