Ryan,
Yes, Autotune is correct. Using the domain as just "site.com" allows you to use your Facebook app on
www.site.com, blah.site.com, and othersubdomain.site.com. It's simply the most flexible setting, and shouldn't hurt your ability to run on any one specific subdomain (www) either. Your Website URL should be
www.site.com though, if that's what your SSL is keyed for, but that's not as important in the App scheme of things.
azwanz,
Your question isn't really related to this topic (Ryan and I got off course as well...). In the future, please create a new topic. For AceSEF, I don't have any specific suggestions, but try ordering the JFBCSystem plugin after the AceSEF (and any other SEF) plugins. It's possible that may help by ensuring AceSEF is ready to parse the URLs, but no guarantees. Honestly, you can try setting the JFBCSystem plugin before it as well, just to test. After each time you change, clear the Joomla caches and use the Facebook Debug Tool to check what JFBConnect is inserting:
developers.facebook.com/tools/debug
Simply clicking the Like button after you change the settings will likely still use the 'old' value. The Debug Tool will clear Facebook's cache.
If that doesn't work, create a new thread and we can help you further.
Thanks,
Alex