Deleting TWLoader files seems to help negate potential problems later, so just delete the _nds folder before doing anything else. After that, download DSiMenu++ and DSiMenu++ Launcher. The contents you need to put on your SD card from the DSiMenuPlusPlus archive you get from github are the "_nds" folder, the "roms" folder (just a central place to store your roms, not really required), the "cia" folder, and "BOOT.NDS". Other than that, if you want to be able to launch DSiMenu++ from Hombrew Launcher, you also need the "3ds" folder.
After copying those files and folders from both archives, install the "cia" files from the cia folder. There should be 3 of them. Then you can use the launcher from your home menu to launch DSiMenu++.