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I have searched for this and haven't seen an answer.

I am creating a Master Page with a header, footer, background and CSS menu on the left side. When I create a content page, the CSS Sub Menus are behind the content. Am I missing a setting somewhere in the CSS menus or when setting up the Master Page.

Thank you for the help

By design, a master page is always behind all other content.
But you can add the menu to a page header and set the stack level to 'in front of content'.