Dear Murat Arpat,
1. If you want to show 5 column in megamenu, you can configure in 'YT Menu Params for this Menu Item' tab.
Example, in our demo, sub-menus of 'Resources' display in 3 column.
If you want display 5 column, please go to 'Resources' and config Advanced Options->'YT Menu Params for this Menu Item' -> set: Number of Columns: 5 , Content Width (px): 1250px, Column Width (px): 250,250,350,200,200
Then create 2 menu items is sub menus of Resources, in every menu, you can load a module or positions in 'YT Menu Params for this Menu Item' => Mega Content Type
2) How can I customize the headers in those positions, for example; background color of header for mega1 position would be black, for mega2 red, etc.
Megamenu don't support change background color in every menu header.
Thanks