External HD Backup Problems With iTunes

I am using 2 externial harddrives with my movies, music, and tv showes, books etc... which i run in itunes so they are all orginased in an itunes folder I am using 2 harddrives because I dont have enough memory on my computer. all the files fit on one but i got an extra so i could make a back up of the other encase something happened to the only one i would have had

My question is this There are some files i want seperate from the other harddrive so when i get lets say a few movies, or music, and i cant remember which ones but know i need to make a backup and want to copy them to the other hd to have a backup I dont want to do a mirred copy to the other. so what i have been doing is copy and paste say the movie file and paste it to the other hd movie file it will then say some of the files already exist do you want to copy over them or something similar if i say no it will cancel the whole thing if i say yes it will copy all the files over the old ones and take forever. I hope im still making sense! sorry for any confusion ! is there any way to only copy the files that dont exist on the other harddrive to the other ? I dont want to just copy the itunes folder because it would take forever to copy all of the files over and most of them are already on the other to begin with just a few songs i dont have on one but not shure which Any help will be appreciated