Hello Bridgecom.
1: You can create a menu of your own. Or choose a different menu for the left menu. It is up to you. Create a new menu and publish it in the left column and unpublish the main menu which is now located in the left column.
2: You need to upload your logo to this folder:
http://www.cambriamagazine.com/joomla/templates/ja_xenia_ii_shopping/images/
It is also important that you call your logo the exact same as the one you are replacing:
logo-default.jpg
Otherwise it will not automatically replace it. 🙂 You can call it something else as well but you would then have to change the name in the index.php file as well ( index.php of your template that is )
3: Changing the colour from the red brick to a different “red” type is something you would need to change in the CSS styling. You would have to replace a whole lot of colour codes. 🙂 So not just an easy switch. You can switch easily between the 3 colours Joomlart have provided with the template, otherwise you would have to work with your template_css.css file to modify it to look the way you want.. 🙂
Hope this has helped somewhat?