You should be working from within the DATA folder - I usually rename the existing game folders "meshes" to something like "xmeshes" and then only work with my mods folders that will correctly be labled as "meshes". Have your archive tool opened up and drag your "meshes", "scripts", "textures", etc. into the archiver, it will pull all subfolders and files into the window. Make sure you have your checkboxes clicked as per the link above and create to the desktop. Once it is done be sure to delete your folders and correctly rename the indigenous files. This process has worked very well for me. Sticz