I take a minute's worth of video at the end of every mosaic run, and put the lens cap on to do another minute of dark. Thanks to some of the guys here I've switched to Autostakkert from Avistack, which also lets you create a dark and a flat file, which you load into the code before processing the image runs and it manages it pretty much automatically.
I've got a couple of solar mosaics using this technique at
http://astrobin.com/users/alocky/
Including a venus transit one.
cheers,
Andrew