The configuration tool works fine for many people.  Did you try typing in the showconfig cheat to see the options in-game?  If showconfig doesn't reflect the options which you chose, then make sure that your configuration file is named "AweConf.package" (not AweConf.package.txt or AweConf.package.xml).  Be aware that your operating system may be hiding the real file extension from you, but the game will refuse to read any package which does not have the .package file extension.  If your file is not named AweConf.package, then that is not a bug in the configuration tool, but in your internet browser.

The other alternative is to create an XML file which contains your selected options, then package that XML.  If you aren't sure of the format, you could extract the XML from the AweConf.package which you downloaded, make changes to that XML, then repackage it into the original AweConf.package.  Of course, this won't help you if your configuration file does not have the correct file name.

That's correct, there are only two files: awesome.package and aweconf.package.  However, you said that awesome.package is working and aweconf.package is not.  This can only happen if something has gone wrong.  For example, your download may be corrupt, in which case downloading it again should fix it.  However, it sounds like you are having this problem consistently, so I was looking for another explanation for your problem.

One thing that people have reported is that their browser adds either .xml or .txt to the downloaded configuration file, so that it is named aweconf.package.xml or aweconf.package.txt.  The game will not read these files; it will only load files with the .package file extension.  The operating system can exacerbate this problem by hiding the file extension from you, so that the file appears to be named aweconf.package, even though it isn't.

If this is your problem, then removing the extraneous .xml or .txt file extension should solve your problem.  I would also recommend changing your system so that file extensions are never hidden.  On Windows XP, you can change this option by running the Windows Explorer and choosing Folder Options from the Tools menu.  Go to the View tab and uncheck the option named "Hide extensions for known file types".

Some browsers will (incorrectly) add a .xml or .txt file extension to AweConf.package.  If you remove the extraneous extension, the game should be able to read the configuration file.