The whole idea behind this is to compile the new MySQL server with different TCP/IP ports and Unix socket files so that each one is listening on different network interfaces. Compiling in different base directories for each installation also results in separate compiled-in data directory, log file, and PID file location for each server.
You can run multiple servers on Windows by starting them manually from the command line, each with appropriate operating parameters. You also have the option of installing several servers as Windows services and running them that way. General instructions for running MySQL servers from the command line or as services are given in Section 2.4.8, “Installing MySQL on Windows”. This section describes how to make sure that you start each server with different values for those startup options that must be unique per server, such as the data directory. These options are described in Section 5.6, “Running Multiple MySQL Servers on the Same Machine”.