The thing is, the bug that Wad Manager uses to work is fixed in System Menu 4.0. Fortunately there's an app out there that uses a closed-source exploit to downgrade IOS35 to a version affected by what's called the Trucha bug, which is what lets Wad Manager work. So you use this app, tell Wad Manager to run off of IOS35, then use it to install a cIOS Wad. After that, you install a patched IOS60 so your installed wads can run from the SD Menu and you're home free. Search for a 4.0 downgrade guide for more info on this:
But NOTE: Some LU65 Wii's are "unsoftmoddable." That is to say that downgraded IOS's don't work with them, meaning you won't be able to install cIOS with this method (and you run the risk of making IOS35 not work if your Wii doesn't like it). I think that WiiGator's cboot2 will eventually get around this problem if it hasn't already.