Here is how I went about doing it:
1. Use DOP Mii to check and see if you have boot2v4 if not install it
2. Run latest Hackmii installer to install HBC 1.0.8 and Bootmii IOS
3. Run cIOSr20 installer and install cIOS to slot 213 base 38
4. Run Nintendo Update from SM
5. Launch HBC and run DOP Mii, select IOS213 to use and delete the stub IOSes in slots 222,223,249 and 250
6. Run cIOSr20 installer using IOS213 and install cIOSes to the slots/bases of your liking.
7. (Optional) Install Priiloader and enable hacks.
While I am not going to comment one way or another on if and why you should/shouldnt update these are the steps using the minimal amount of programs needed to have an up to date SM, IOSes and Channels.