Well, you can change some things "in the hand" just like you said, or you can use 2 ways:
By the Bootstrap website
Through the Bootstrap website, there is a page called "customize", there you can change some class states as well as colors, fonts and everything else.
http://getbootstrap.com/customize/
That it already gives you . css and . js ready for you to use in your project.
that by default he uses the LESS to "compile" the css
Downloading the "font"
If you prefer you can download the "source" of the bootstrap and "compile" it using the SASS or LESS
Through this Download
Extras
There are websites that you can style components in specific bootstrap like:
Or if you prefer a visual editor
Your CSS file is linked below the bootstrap CSS?
– user13603
Edit the question and add your code - which is related to the problem, not all of it. Without the code it will be impossible to tell what is happening.
– Woss