How do I deal with the custom part when I use Bootstrap?

Typically, you override the CSS. I think we can change the loading order of CSS rather than using !important.

First, load the CSS of Bootstrap, then load the CSS of the changed theme.

If duplicate settings exist due to CSS characteristics, follow the last declared statement. However, for properties defined as !important, it can only be overridden by !important.

Here is an example. Example of overriding the class of CSS defined in bootstrap using tags after css loading. A simple example of changing the color when applying navbar-inverse to the navigation bar of the bootstrap.

<link href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css" rel="stylesheet">
<style>
.navbar-inverse {
  background-color: #248
  border-color: #103070;
}
.navbar-inverse .navbar-brand {
    color: #eee;
}
.navbar-inverse .navbar-nav>.active>a, .navbar-inverse .navbar-nav>.active>a:hover, .navbar-inverse .navbar-nav>.active>a:focus {
    color: #fff;
    background-color: #103070;
}
</style>

I think it would be better if you design it by making changes overall like the above, or borrow the ones that have already been designed, such as https://wrapbootstrap.com/ and modify them.

If you do simple customization, the method that Heo Dae-young told you is the simplest, and at first, you will use this method the most.

If you want to customize in detail, you can set it to your liking at http://getbootstrap.com/customize.

There is also a http://bootstrap-live-customizer.com site for easier viewing.

If you're more professional, you can customize a project like bootstrap/bootstrap-sass. If you get used to css a little, I recommend you to move on to a preprocessor like sass. There will be a lot of difference in productivity.

Reference

(Almost all cases) Avoid !important.

If you just understand the priority of css selector and use it, it will be much easier to maintain the code.

http://bitsofco.de/on-not-and-specificity/

I recommend this place. You can test real-time by changing colors and fonts in real-time, so it's good to use without having to peel the core ends. Note that only version 3.3.6 is supported. http://bootstrap-live-customizer.com/