1- The search icon is standing out because it’s styled to match the mega-menu style we used here: http://themes.creiden.com/circleflip/
while here you are using another style which we didn’t apply for the icons out there.
2- Uber menu is not included in Circle Flip bundle as it’s not available for extended license. No wasted money here 😀
3- To choose our style of Mega Menu, please head to the Theme Options -> General Settings -> Header Settings
You’ll find few styles for the header, the last one has Mega Menu support. Please try it and let me know if it works well for your structure as I realized that you have a different structure for the menu than the one we have.