1) The directories are designed to be used for various bits of code. In general, Layout is for subtemplates and Includes is for code snippets that can be included in other templates.

2) Yes, that should work, depending on how the template is set up.

3) It depends. If the text is embedded on the image, you'll need to clean that up. If it's set up through a menu controller, then you'll need to edit the menu control and possibly the page names.

For 1) you might also want to read the docs on the sublayouts - http://doc.silverstripe.org/html#layout

Silverstripe Templates as page.ss can include sub templates such as menu.ss, content.ss and so on. It depends on the template and general layout of the specific site.

If you would like to use addtional javascript or stylesheets you should put them in the right page controller

e.g.:

class My_Controller extends ContentController {
public function init() {
parent::init();
// added some Script
Requirements::javascript( "mysite/code/myScript.js" );

As it looks, the top red menu on you're page could probably changed by changing the navigation label of the corrosponding page in the template.

If you need further assitance in you're Project you can contact me at emil.blume[at]gmx.de or even if there should be done some work.