Sorry for the late reply... the release of FCP X had me rather busy... Here's some instructions:
1. Launch Compressor. If you get a New Template dialogue choose "Cancel".
2. Open a Finder window and navigate to the location of the audio files you wish to batch convert. Select them all and drag them into the background of the area of Compressor titled "Drag Settings and Destinations here".
You should see all the files now listed there.
3. In the Settings pane choose the "Settings" tab and drill down into the folder:
Apple > Audio Formats >
Single-click "Aiff file"
4. In the Inspector you can see the parameters for the 'Aiff File' setting. At the moment this preset cannot be changed, so right-click on "Aiff File" in the Settings area and choose "Duplicate" to create your own Custom setting.
5. You should now have 'Aiff File Copy' selected. You can change the name in the Inspector if you wish.
Now click on the second tab (Encoder Tab) in the Inspector set your desired file type and then click on the Gear icon. The 'Channel', 'Sample rate' and 'Sample Size' can now be changed.
For example, you may wish to change the 'Sample Size' (Bit Depth) to 24.
When you're done making changes to the format choose 'Save'. Now your custom setting will be saved for the future :)
6. Drag the Aiff File Copy (or whatever you called it) onto all the files in the top left pane.
Tip: If they are all highlighted (selected) you only need to drag the setting on to one of the files.
7. You may wish to choose a destination (from the Destination tab in the Settings pane) and drag it on to all the files.
8. Now click the 'submit...' button and choose a name for your Batch jon - although this isn't too important.
If you didn't choose a destination then the converted files will all be placed in the same folder as the originals.
Next time you do this process it's a lot easier as you've already created your custom setting!
Hope that helps,