Hi
Regarding the top header position that is the position where are published 3 modules 1) The logo – 2) The social position with the three social icons – Facebook – Twitter and the Rss 3) The search module
If you want disable the entire block you need to disable your logo the social module and the search module
anyway the file that manage the header is in this folder pluginssystemjat3jat3base-themesdefaultblocksheader.php
Regarding your second question the positions absolute and top-panel are disabled because now are empty
To verify this make two custom-html modules and publish it in the absolute position and in the top-panel position