2 github repositories on the same project

Does one folder contain the other, or they are completely different?
You can't in the first case: https://youtrack.jetbrains.com/issue/IDEA-64024
And you can in the second, just add the second folder as a VCS root.

Its 2 plugin folders so yes they are not under eachother in any way.

Any guide as how to do this? (besides Robertyeo's answer https://intellij-support.jetbrains.com/hc/en-us/community/posts/206354859/comments/206951095  )

I followed his answer and created another VCS root but how do I connect it to a different github repo so it does not commit to the first existing repo?

Thanx

Select VCS > Git > Remotes. You can specify remotes there individually