If you go to your admin panel and click on Site HTML, you'll see the following:
1. Top of Page HTML Editor. This is where you would put the coding for the top of the page (don't use head tags or body tags). This is where you would enter the code to pull up your banner and any top of page horizontal navigation, etc.
2. Left Column HTML Editor. If you don't want to go with the standard draw functions found elsewhere, you can use this to custom code your left column. You can also do a combination of both custom and MC-generated code (

-generated = Site Layout > Left Column Display Options). For example, I use the

-generated Search box, but the rest of my left nav is custom coded.
3. Right Column HTML Editor. Same as above.
4. Homepage Messages Editor and Homepage News Editor. These both control the center content on your homepage. You can custom code whatever you want here.
5. Bottom of Page HTML Editor. This controls what appears on the bottom of every page.
You can also eliminate any right or left columns elsewhere in the software, depending on the look you want.
Play around with it a bit and see what you come up with.
You can also post your domain here and see if anyone can help you with specific questions.