As my expreince, not very different from what you have expreinced was, older versions Xfree autodetection was not very good but still attempted, on the other hand X.org autodetection is very good, if I remember correctly it was creating a *.conf file somehwere in / or /root but you can always check the logs to see which conf file it has used
"Any fool can write code that a computer can understand. Good programmers write code that humans can understand." --- Martin Fowler, Linux User: #416714