Hello - there are a lot of questions here - maybe next time break them up.
But in a nutshell - div means area (division) - if you remove a div (like header) you will remove that area including the areas and images within it. Take another peak using firebug and you will see all the divs inside the header div. Click on the plus button to open - the button is in FB next to the <div='''etc - that is if there are elements within it.
So, for example in your template, there is another div (area) within the header div - called logo - the logo image is in it. While you find it difficult to change the entire header many people my only want to change eth logo image - so it makes sense to separate the images in this respect - but ultimately - if you want to make a lot of changes you do have to know the language a little (html / css) and perhaps even some php.
Many commercial templates will come with some instructions for how to change the ogo and basics - this looks like a rockettheme template and they usually have documentation and forums. And usually someone has already had the same problem as you.
I agree though that by providing so many options (to please teh masses) there can be more complexity in customising etc.
WRT to the menu – can you not unpublish the menu from that position?
Images – if you right click on an image you can view image and this will show you the path to the image
if you click on an element – the right hand side of firebug screen will show you where the styling code is.
However, in the case of mods and stuff some styling may be within the module itself and you may have to do an override etc.
So when you click on hotdeals the div then view at bottom – you can click the plsu sign next to module table to see more and the styling will be on the right
Ps: Your template is looking a little crazy – but Im assuming that's because you are working on it.
