I checked your website, 1) yes, the columns shortcode does not suit long article:
I think you need a page build.I have installed Aqua Page Builder and Black Studio TinyMCE Widget in your site. You can try to edit a article by page build/Black Studio TinyMCE Widget.
2) I did not find the menu messes up the whole layout. I don’t understand your question, could you paste a screenshot? I can check again.