Ah, you're making progress :-)
Do you have a shutterless camera? If so make sure to tell MaxIm to use that dark filter slot for a shutter.
Anyway good question. You'll need to make the dark "filter" the last in Maxim's list. This has the advantage of keeping it out of the way on the web forms. Then when running FilterOffset.vbs, temporarily blank out that filter slot in MaxIm, like the other unused slots, so that the script won't try to use it. Once you have the offsets completed, you can go back in and put the Darn name into MaxIm. ACP gets its filter names from MaxIm every time it connects to your camera.