Pyrus has two kinds of configuration files, system configuration files, which are stored directly in the installation location, and user configuration files, which are stored in the home directory of the user, or in the Windows equivalent, My Documents.
Each installation is tightly bound to the configuration that defines where files should be installed, which PHP executable to use, and which php.ini is used to manage that installation.
On the other hand, user-specific preferences are tightly bound to each user, by placing them in the user's home directory. These values are universal to all installations and include things like the amount of information to display, the preferred mirror to use for a channel, the openssl certificate to use for package signing, and so on.
This way, multiple PEAR installations can be managed very safely without ambiguity over what configuration values should be used.