Not everything will be affected-- for instance, you probably won't need to reinstall your bootloader, except for really big updates (such as the jump from Mavericks to Yosemite).
However, you will have to reinstall the following every time you update Mac OS X: And that's all there is to it!
Once you have reinstalled the appropriate drivers (whether through Multibeast or anything else), you can restart Mac OS X.
Minor updates are usually fine, but full OS upgrades requires updated Clover bootloader and other things like kexts and shouldn't be done on a whim.
With the yesterdays introduction of Kaby Lake to the Apple computers line up things should start working well in the future. If you want 24 hours there will be plenty to read online to see if an upgrade is OK.
I'm on mobile and not fully awake yet but I had to do the same for my Lenovo P580 laptop to get graphics working.There are two main ways to install a Mac OS X system update.The first method is to update your computer directly through the Mac App Store.My setup works fine using the Skylake CPU id and the GPU id, it worked fine for months but the last update seems to break it, at least for me.Once updated i can't continue using fakegpuid. Many of us upgrade straight away and then get vocal online when stuff don't work.