We'll turn this into more of a real tutorial later...this is a very fast bried on the issue...
When customizing your Indexhibit site it is very important to know that you should not ever adjust the paddings #menu or #content. And for that matter, unless you understand what you are doing (knowledge of the box model and more specifically how the template works) you should not be adjusting the margin settings on #menu and #content as well.
How do you add padding then?
Simply use .container but you can add rules to target specifically the container for either the #menu or #content divs. Like this...
#menu .container { padding: 21px 0 21px 21px; }
#content .container { padding 21px; }
A clarification - when you see four numbers for the padding it starts at the top and works it way around clockwise - top, right, bottom, left. When you see only one number it represents all four at the same time.
By understanding these relatively simple rules you can avoid a ton of confusion and messed up displays of your site.
We'll add more to this over time. I'm adding this to the Useful Threads post as well.
Please do not ask questions in this thread - it is purely for information. Thanks.