When you type a branded term in Google search you will get the top result with some of their most popular sub links. I wanted to know if using a good structure helps Google determine which links are the "main" links and which ones they will show.
That's a bit of a different question. They are called "Site Links" http://support.google.com/webmasters/bin/answer.py?hl=en&answer=47334 will help you to understand how those work.