I assume that you are using Portal engine templates. If I am getting the right meaning, you want to have different section of the web site with different layout. To achieve this, you can change (or break) the page templates inheritance from the master page (http://www.kentico.com/docs/devguide/visual_inheritance.htm
), so each page which is not inheriting the content and layout from parent(s), can have different layout.
Also, if you want to have different picture (or flash, etc) as the main logo for different sections, you can take inspiration here - http://devnet.kentico.com/Knowledge-Base/portalengine/Using-different-graphics-for-different-site-sectio.aspx
I hope this is what you need and that it will help. If not, could you describe your need with more details - e.g. some example of the site structure, etc.? Thank you.