Usually the first thing I do after selecting the images/avis to process is to tell Registax which darks (and flats) to use. Once that is done, then launch into selecting alignment points.
I'm not sure if it makes any difference if you add the darks later, I haven't tried... but I have a sneaking suspicion that the darks are subtracted as the alignment process if done. I'm not sure though

... the only reason I say that is that I have a recollection of hot pixels disappearing during the alignment process when using darks.
Please correct me if I'm wrong, if anyone knows better!
Hope this helps.
Al.