As is indicated in the instructions file, you should first find the location the mod package installer installed the nude skins to under your Localdata\texture_library\... folders, then copy over the .wtex file(s) you want to mod, use the WTEX2DDS.exe to take one of the .wtex files, convert it to .dds, then edit that .dds with whatever edits you want (or just overwrite that .dds with an edited one you already have), then convert it back to .wtex and copy it back over to the appropriate Localdata\texture_library\... location, overwriting the old file with your new one.