OK a few things:
1. You should not edit UI.X directly with your changes, when it comes time to upgrade you will find it quite difficult. Make a child theme, hide UI.X, then make all your changes to your new child theme.
2. A simple solution to your logo problem is this:
Code:
.hasSearch #logo {margin-left: 0; margin-right: 0;}
However, that margin is there in the first place for the search icon. Doing the code above might make it so your logo interferes with the icon. Judging by the type of logo, it will not though, its just there is a better way of doing this.
First I would separate the main logo from the background. Then I would set the background to #logoBlock and then use the cut out logo as the actual logo (then remove the code I posted above)
Whichever way you go it should be OK though. So if you want to just copy that code into EXTRA.css you should be all good to go.