First of all, Handbrake is unreal in that it is free. What an amazing piece of software. There are a lot of guides, but a very practical tip sheet can be found at https://mattgadient.com/2013/06/12/a-best-settings-guide-for-handbrake-0-9-9/
For me, I have one tip to add. Often, I want to encode something, and I don’t want it to use my entire CPU. It heats the computer up tremendously (though it’s ok to do that), and turns the fans on all the way. Instead, I rather my MBP work with half on, and half resources for other things. Usually, that means I’m still not waiting on anything. But they never tell you how to not just go 100% on Handbrake.
In “Additional Options”, add the following:
If you do this, it will only take up half, and leave your computer more usable. If you’re running overnight, and you want it to get done, don’t add this. Try it, and you’ll see that in certain instances, this is helpful. Enjoy.