1) how to delete/make invisible the header box that contains the logo. we need the logo not to be in box.
— Do you mean to remove the background and box shadow, then you can add the following CSS in “Appearance => Theme Options => Custom CSS” box.
.site { background-color: transparent; box-shadow: none; }
#main { background-color: #fff; }
#homepage-message { margin-top: 0; }
2) How to center the logo on top of our website.
— Just add the following CSS in “Appearance => Theme Options => Custom CSS” box
#header-left, #site-logo { width: 100% }
#hgroup-wrap img { margin: 0 auto; }
3) We need the submenu of the main menu to open vertical. how to do this?
— This option is not there in theme. You need to hire CSS developer to do this for you.
4) we need to place 2 widgets in footer that contains news from 2 different categories and the title of the widgets to be centered and not alligned left as they are now.
— This options is not there in theme. You need to search for plugin to do this or you need to hire developer to work on it. I have only help in CSS alignment.