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The better case is that the logical structure matches the physical structure, which means:
Homepage link to all Channel homepage (set homepage for A,a Connect to BCD)
The home page is generally not directly linked to the content page, unless you are very interested in pushing a few special pages
All channel home pages are connected to other channels home (B C D interconnected)
The Channel home page is connected back to the site home page (B C D is linked back to a)
The channel homepage is also connected to a content page that belongs to its own channel (for example, the content page EF, B is connected to E and F pages)
The Channel home page is generally not attached to a content page that belongs to another channel
All content pages are connected to the site home page (E and F are linked back to a)
All content pages are connected to their own top level channel home page (e,f back to B)
Content pages can be connected to other content pages of the same channel (E can be connected to F, for example: "Next page")
Content pages are generally not connected to other channels
Content pages In some cases, you can connect to the content pages of other channels with the appropriate keywords
The Channel form the topic (if C channel has h page, E page can link to H page on a key word)
What is more important to search engines is the logical structure formed by links.
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