There's probably a way to do it with Mystcraft or RFTools and some hackery (such as by replacing the contents of the folder for some random RFTools/Mystcraft dimension with the atmospheric effects you want with the contents of the Overworld dimension folder of the dimension you want to copy over), but that's not really my area of expertise. There may be a better way to do it that I don't know about.
However, I do know for a fact that the above will not work if any changes were made to the pack at all between the creation of the worlds you want to merge. If you created and built up a world in one dimension, updated a single mod so as to use a single additional block or item ID, and then created your other world, there's a better than even chance that at least half of all the block and item IDs will get screwed up when you copy the dimension files over. If the world even loads after that.
You have been warned. If you try this, do so very carefully, and make lots of backups.