No its a straight forward subtract using the "Image math ..." menu item

Take a look at this link as it summaries other sometimes better methods - http://tinyurl.com/24dfxy

Finally Deep Sky Stacker (free) written by Luc Coffier (he posts here) is making progress on automating stacking comets. Keep an eye out as at some point soon I'll review DSS's comet handling here (maybe in 3/4 weeks time)