As Michel suggested you should place all your resources (such as config files) in the resource folder. This keeps a nice and clean project folder and the modeler will automatically include all the files from the resource folder into your deployment archive.
Like you said the default working directory the runtime uses is kind of unpredictable. But you can ask the runtime the location of the resource folder to get the path to your config file
String pathToConfigFile = com.mendix.core.Core.getConfiguration().getResourcesPath().getAbsolutePath(); pathToConfigFile += "/MyConfigFile.config"; return pathToConfigFile;
You should put such files in the resources folder. Then you can then use the configuration api to find the correct folder