They're really completely unrelated. And both are pretty safe as long as your power doesn't go out while you're installing them. That's really the only risk. However, I don't know that either of them will let you play Wii Music. You probably need to install a couple IOS files. What error are you getting when you try to boot it? Or is it just trying to get you to update? If you have some sort of software booter that will bypass updates (I've only used USBLoader and a modchip, so I'm not sure, but maybe GeckoOS allows this?) try to boot it with that. If that doesn't work, try installing some of the IOSes, like 55 is known to be required for some games.
But Waninkoko's 4.0 allows you to update so that you can gain the additional features of the 4.0 firmware (mainly playing WiiWare off an SD Card), while Preloader is more for brick protection and some random system hacks. Actually, I think one of the system hacks lets you bypass updates...