Their manuals start with a list of parts, including the part number. You can see that number in the build steps too. If there are two parts that look alike, you can put them in two separate piles next to each other, so you know you should check if you've got the right one when you need a part of one of these piles.

I usually sort all the different small parts at the beginning of building something. It's nice to know that all the parts are there and you don't need to search for them.