Question about Siloing

Hey all, I just signed to WF . I'm also starting on SEO world by reading SEO for dummies book but I'm hitting a brickwall now. For a website siloed like this:

Main theme

• Main Category 1
  • Sub cat1-1
  • Sub cat1-2
  • Sub cat1-3
  • Sub cat1-4
  • Sub cat1-5
• Main Category 2
  • Sub cat2-1
  • Sub cat2-2
  • Sub cat2-3
  • etc..

From where to where should I be linking my content? For what I've read I know all Sub cats should link to their Main category landing page and to each other (on the same silo). What I'm going to ask maybe is really newbie but I'd also put links to my sub categories on my Main Category page to show to my visitors where to find those subpages, is that right? (on Main category 1 have a link for sub cat1-1, sub cat1-2. etc?)



Also, I'm not sure what to do with navigation menus and Silos. Let's say I have a top menu which is present on all my pages with links only to Home and Main categories. In theory that shouldn't affect Silo because I'm only linking to a Category landing page right? What if I also add subcategories on a dropdown? In that case my relevance would be affected in a negative way?


Long story short, from where to where should I link my categories with my subcategories and how navigation menus could affect my rankings?


Many thanks in advance for your help