Bootstrap considers two different types of customizations. These customizations can either come from yourself, and/or a 3rd party.
Light customizations – which include changing minor things like color and font changes.
Overhauls – which change the way a class functions.
Make sure you find the Bootstrap selector, and use the same selector. This keeps you from having to do things like use !important.
Additionally, you can add your own classes to add styles to your own website, and keep them looking the way your design would have them look.
Additional Customizations
Additionally, you can use the customizer tool, http://getbootstrap.com/customize/, which will allow you to cut down on potential bloat. Here you can select which components you wish to include/exclude as well as define the color schemes by using an online version of {less} variables to define colors and other parameters.
This will keep your downloadable file sizes smaller, but you will need to locally host your files instead of being able to host them on a public CDN.
Customizing and Bootstrap Themes was originally found on Access 2 Learn
