When I use LR/Enfuse I usually group the images into stacks with the image with the highest number at the top of each stack. In Enfuse I add the suffix '-blend' to each combined image as a way of filtering out blended images (i.e. DSCF35278-blend or something like that). Enfuse adds the completed composite to the same stack.
Enfuse has several different uses, including HDR blends: http://www.wolfnowl.com/2011/10/using-the-lrenfuse-plugin-for-lightroom/