You'll have to be a little more descriptive... what specifically are your problems?
I see that the "bottom" section (I take it you mean the footer section?) has two divs-- #footer (which isn't closed) and #footerdefault. I'd take a look at that first.
As far as your other issue-- how to mark up things with proper "naming conventions"-- the simple answer is to mark things up as what they are. It's essentially the essence of any mark-up language.
For example, a paragraph should be marked up as a paragraph, a list as a list, a citation as <cite>, a block-quote as <blockquote>, an address as <address>, etc. Divs and spans are meaningless elements; they are used to denote a section (division) of the page to group elements in (or, in the case or span, to apply styles within an element, like "<p><span class="intro">An introduction</span> is sometimes styled differently within a paragraph to draw the reader in.</p>). So if you have a header, a descriptive paragraph, and a list of links in a navigation section you could mark it up like so:
<div id="navigation">
<h2>Navigation</h2>
<p>Please select your destination from the list below:</p>
<ul>
<li><a href="/home/">Home</a></li>
<li><a href="/somewhere/">Somewhere</a></li>
<li><a href="/somewhere/else.htm">Somewhere Else</a></li>
</ul>
</div>
Hope this helps...