The preferd way to change the CSS is to inspect the elemtn, find the class and overwrite its css styling via the Admin->Settings->CSS & JS tab. There you can define your own CSS styling overwrite.
For example, let's change the frontpage initial blue theme to red. This is the CSS you need.
.bg-primary {
background-color: #ff0000 !important;
}
​
.headroom--not-top.navbar-theme-primary {
background-color: #ff0000 !important;
}
​
.btn-primary {
background-color: #ff0000 !important;
}
And you can do this for every ID or class inside the html.