There are very few "commands" that actually require the Windows key. For example snapping windows or the fancier tab switcher use the key as does the run command. If you can identify what operations you want to use then it would be easier to simply remap them instead. Remember that not all keyboards actually have the Windows key so there are almost always alternative keys.
AFAIK, out of the box, you cannot remap the Windows key itself. However there are 3rd party apps that supposedly let you do this like AutoHotKey and SharpKeys. These are third party products and would require more software to run on your machine so use at your own risk.
You might also look at the Windows Powertoys Keyboard Manager app. I'm not sure if it can remap the Windows key but it might be a good starting point.
You didn't provide us a link to the steps you were trying to follow so it is hard to say where things might be going wrong.