I think I could help you with this, but you're going to have to be more specific about the scope of help you need. Maybe if you posted code you have tried changing or inserting I might understand what you need. It seems pretty simple though.
It seems like in your first question you are just asking for two links:
Code:
<a href="<article directory url>">Article Topic Directory</a>
<a href="<main website url>">Main Website</a>
As far as your second question, a short INSERT statement should solve that problem. Do you need help writing the SQL query?
And finally, I'm not sure what you mean about a "subscribe" section. I added a plugin on my own website (pretty easy to add plugins) to allow people to subscribe to comments. Beyond that, it might be a little bit difficult to code by hand.