using "external url" for category urls: some doubts

I tried to read carefully this article

http://www.mintjoomla.com/community/knowledge/user-item/43-sergey/245-create-joomla-menu-links-to-categories-or-itemid-understood.html

and here is my current situation

Right now there is no category links with individual itemID. it is a limitation of Cobalt. It was not intended that Cobalt category links inserted into menu. Or even if inserted only as subelements of section menu and without need for individual modules one every category.

We will try to add this features if we can. It is hard to make because it will require users to understand what they are doing otherwise it will lead to double content URLs on the site.

I guess for now the best solution would be to create different cobalt sections for each menu item you want in the site main menu

I thought a structure like

main-section

category1

subcat1

subcat2

category2

subcat1

subcat2

would be better and more easy to manage

maybe I should instead do something like

section1

category1

category2

section2

category1

category2

maybe the problem is just that I am trying to build sites using ONLY cobalt, even for those areas where joomla default pages could do the work

so doing this it's obvious that I will end up creating main menu items using cobalt categories

I guess for now the best solution would be to create different cobalt sections for each menu item you want in the site main menu

That depends. If you want to search through all of them then not. You know that advanced search only in one section. So there is dilemma and it depends but I would not base section structure only because of menu preferences.