I think I understand your problem.
In fact you have two I think.
First you should use a contruction like this:
<div style="position:relative">
<div style="position:absolute">
"Your site"
</div>
</div>
This will make the site appear below the page settings row.
Second is the fact that in a way the modules "grow" if you look at them in admin mode.
Since you use absolute positioning they will overlap.
There are two solutions for this.
1. Don't use absolute positioning but use relative (you cold figure that one out yourself I guess)
2. Create a pane for every module and set overflow to auto for the panes.
If the module gets to big for the pane you will get a scroll-bar. This is als safer if you use modules that can grow if you edit them like a menu that can become longer if you add more items.
The layout will stay intact and you can reach the modules.
Not ideal but it's better then the way it is now.
I never found a good solution to load a different stylesheet for te admin
It would be nice if DNN would render this:
<div class="username">
the website
</div>
Then you could make a skin that is different for different users
But it doesn't
Hope this helps