The way elements are arranged on screen carries lots of meaning that we interpret subconsciously when decoding web pages.
The relative positions implies relationships on lots of different levels.
The key is to make sure you represent visually the correct relationships.
Layout tools
You can use tools like contrast and spacing to help differentiate elements.
Other techniques are useful for visually associating similar elements.
These techniques are often used in combination - when you group a collection of links, for example, you also differentiate the group from the elements around it.
Techniques for creating associations
Associating elements implies a relationship of similarity, e.g. A, B, C are a group of equivalent 'peer' elements.
Groups can be created using any combination of the following mechanisms:
- Containment - making one or more elements literally part of another element
- Grouping through Proximity - is like containment with invisible containers
- Alignment - aligning elements along visible or invisible lines
- Rhythm - creates relationships through repeating stylistic features

For instance, 'Containment' is the first link in the paragraph but isn't the next topic in the navigation. In the navigation 'Containment' is the third topic.
Right now as user I am thinking:
-Should I go to 'Containment' as the author seems to have placed some importance on it by putting a link, the first link, to it in the paragraph?
-Will I lose my train of thought by taking this detour?
-If I do ignore the link this time and just click on 'next' as I have been doing then wouldn't this diminish the effectness of future links in content? I'll just ignore them in the future at the risk of ignoring something that the author thought important.