How to properly add Bootstrap and JQuery Javascripts?

WordPress loads jQuery because plugins and themes suppose it does. If you want another version of jQuery for your theme, there is a risk that plugins you may be using will not work, since (if they are maintained well) they are designed to work with default jquery.

That said, if you insist on using your own version of jQuery you can easily deregister it, as you found out. If you’re not planning a public release of your theme you can control the consequences.

And yes, you should enqueue styles as well. The reason to do this, is it allows you to set dependencies, which is important if (for instance) you would want to make a child theme and deregister the parent styles.

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