I received the bonus points for doing reviews in the marketplace, but starting on 9/1 they separate my DA points, and bonus DA points. Which is great for tracking, however you cannot check out using bonus DA Points. So how are we supposed to use them? 

You are referring to Paid Points, right? Those are prioritized over Earned Points automatically with purchases at Marketplace (in my case at least)... Unless you meant something else.

So I have to use my paid points to use my bonus points?

See? Why can't I use my 4k bonis???

I figured it out. There is a checkbox with small print to apply bonus.