ok here is a simple way to update your SM Get the Homebrew app called Dop-Mii Wiibrew Edition and use that to install your SM and that's all. All your homebrew and softmod stay in tact. simple and easy i promise you this is all i did.
Simply load up Dop-Mii Wiibrew Edition
Install SM of current Region
Reinstall Priiloader if you had it installed previously
done and done i was curiouse about updating to the newest SM and this is the safest and best way to do so just get the .wad file of the SM you want from NUS or do a online install like me.
There is nothing wrong with Waninkoko's Updater but there are better alternatives out there now.
Personally, I'd recommend doing some reading and learning how to update your Wii manually. Learning what IOSes to download and which to patch etc. You only need some knowledge about the latest versions of IOSes and apps/channels, an idea of your personal preferences where options exist, and NUS downloader with any WAD manager.
You only really need to download the latest non-stubbed IOSes. Patch the IOS that your System Menu version uses with the trucha bug. Install any other cIOSes that you may want or need like Hermes' v5, Waninkoko's cIOSx v20, and IOS236 (patched IOS36 installed as IOS236). Install the latest version of any channels and the System Menu of choice.....and anything further like Priiloader or whatever floats your boat.
If you have no idea what you want, need to learn more about the options available, or are just overwhelmed, I suggest taking a look at using ModMii. It is easy to use, provides many options, and is a one shot deal. Just read ahead on all the options, choose what you want, and go from there.
For a comparison, I have my Wii updated with all the IOSes from the latest 4.3 update (stubs