lammert - 1:56 pm on Apr 25, 2010 (gmt 0)
The MySQL server and the client are two different software packages and they work independent of each other. You should be fine editing the my.cnf which is used by the client. You may have two my.cnf files now on different locations because your XAMPP installation uses the /opt tree, while the client is /etc oriented.
The client doesn't need to know the directory path where the server or the databases are located. All it does is connect to the server through a socket or through a network connection, depending on the settings in the my.cnf file.