1. Below is a guide article that illustrate all the insertion areas available with or without the Xtreme Plus plugin.
Layouts and HTML Insertion Areas – Weaver Xtreme Guide (weavertheme.com)
If you want something above both content and sidebar, the easiest would be to use the XTreme Plus plugin.
If only above the Content (not the sidebar, you could use the Sitewide Top Widget area.
2. This is because they use full width options
I suggest you read the article about Full width designs so you understand all these new settings
Full Width Designs – Weaver Xtreme Guide (weavertheme.com)
The header and the footer appear to be using the wvrx-fullwidth class, which is likely located in the header/footer class option box, remove that.
The menu is using thee “Align-full” choice in the menu align area option, change that to what you want.