Can background check companies really find out how many places you've worked or is it okay to just put down the best ones you've worked at?

Yes, background checks can find every place you've worked. Plus, if you leave gaps in your empoyment history that will cause questions.

What are you going to do with the gaps in time,

1. when they call these companies to confrim dates worked

And many computer checks will show many of the places that you worked