Sections Pro has a control labelled priority. This affects the stacking order of Sections when they overlap. For the technical amongst you, priority is simply a z-index control. If you are non-technical don't worry about it, this page will tell you all you need to know.
Most times, you will not need to use the Priority control. There are just two cases where you need to think about it.
Here are 3 Sections with some connectors.
Top and bottom Margins are set to auto to space them out and allow you to see what is going on.
You can see that, without intervention, elements further down the page will always overlay those above.
If we take the situation on the left and see how it would look without the auto margins enabled we see a common problem.
This is exactly the same 3 Sections stacks, just without margins. It looks as though the bottom connectors are missing but of course they have just been covered by the green one completely.
Priority is technically the z-index but that is not important. All you need to remember that a section with a higher priority will display on top of one with a lower priority regardless of their order on the page.
We need to add some padding to the Sections to make sure that the overlapping connectors leave space for the content and look good. See the Banded Pages and Angles page for detailed descriptions of this.
Despite having equal padding above and below, out headers are offset towards the top. (The same would apply to Foundation paragraphs and buttons).
This is simply because those stacks have a bottom margin enabled by default. Simply check the remove bottom margin in the Header stack settings and it will be symmetrical.