To get modules to show on your article pages or the accordion menu to not show on the homepage you have to have menu links to the articles then you can specify which modules you want to show on what pages as this is defined via menu links.
So when you open up each module in your site modules admin area you can define on the left hand side if it appears on all pages or just a few by selecting menu items.
I am trying to have the side navigation stay when I click on a new artice I have created, but I am not sure how to add menu links to the articles. I am completely new to joomla sorry