OK, I will try to explain what you're doing wrong here.
When you go to PageLines > Drag & Drop, there are a number of template sections available to you, which are Header, Page Template, Content Area, Wrap, SB1, SB2, MoreFoot and Footer.
The Page Template area and the Content Area are both part of template for example:
Page Template area is your full width page, which means any sections added to this will be full width of your page area.
The Content Area is your main content body, any sections added to this area will be inside your content area and therefore, have the sidebar(s) aligned with them. For Content Area to become active on your template, you need to have the Content Section active on your Page Template area.
For example:
In the screenshot below, I have the Boxes and Content sections active in my Page Template area for my Template | Default. This means that the Boxes will be above the Content area so they will be above my sidebars.
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In the screenshot below, I have removed my Boxes from the Page Template area for my Template | Default but kept the Content Section active. I have then added the Boxes section to the Content Area of my Template | Default. This means the Boxes will be in the content area and therefore, have the sidebars aligned with them.
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