The custom styling can be achieved via css. If you are using Chrome browser, you can right click on search element, select "Inspect element" from the menu and this will bring up the Chrome console, where yu can find which element has what css class. The cse elements have usually classes starting with gsc- prefix. Then you can use those classes to write your custom css. E.g.:
.gsc-input-box {
border-color: purple !important;
}
Here is a jsfiddle example: http://jsfiddle.net/m8Twp/