Here's what I did, and it worked.
TO MODIFY HEADER
Open File:  /templates/base/_sub_header.html
delete ...
 <bx_injection:injection_header />
 <div id="notification_window" class="notifi_window"></div>
 <div id="FloatDesc" style="position:absolute;display:none;z-index:100;"></div>
 <div class="sys_main_logo">
 <div class="sys_ml" style="width:__main_div_width__;">
 <div class="sys_ml_wrapper">
 <bx_injection:injection_logo_before />
 __main_logo__
 <bx_injection:injection_logo_after />
 </div>
</div>
Open File:  /templates/base/_header.html
and add Customized Header to _header file
Add After: <body <bx_injection:injection_body /> >
Note: You may need to delete Cache File to see changes..  Make sure not to delete .htaccess file located in the Cache folder.
Hope this helps you.