First, it's very simple. And it's definitely worth it, mostly because of how our product is upgraded. You want your changes to be additive, and in different new files, because if you modify our files, our installer will boot out your changes on upgrade (though it will back them up).
Open up a Windows explorer window to your ScreenConnect install to get started. Navigate to the App_Themes directory. You'll see the same themes listed there as listed on the Administration page in ScreenConnect. Take the directory of the theme that most closely resembles your eventual theme, and copy it back onto the App_Themes directory. Windows will usually create another directory called "<ExistingTheme> - Copy". Next rename it to what you want your theme to be called. Now you've created your theme. It will appear as a theme on your Administration page.
The Default.css file is the basis for the theme. It usually @imports some base CSS files, then overrides styles. You should modify the Default.css file to override whatever you need. When you define the same style, but lower on the page, it will override anything previously defined. So define your styles below the @imports, and you'll have the other styles overridden. You can even copy the styles from the base CSS files, and just change what you need.
Contents of original Default.css stylesheet from "Plain" theme:
Code:@import url("../Base.css");
New contents overriding background color:
Code:@import url("../Base.css");
body { background-color: Red; }