In my original copy before PowerCMS is applied, I changed the folder name "CSSMenuWriter" to "verticalmenu", then applied PowerCMS content region using PowerCMS Builder, and I saw it added another "CSSMenuWriter" directory. By doing this, both my original front end with CSSMenuWriter vertical menu and PowerCMS admin menu renders properly.
Is there a way to prevent this overwriting behavior from happening? I'm guessing it is a bug in PowerCMS Builder. FYI, I am using the latest version. I reinstalled it earlier today using the file downloaded from Download Center page.