We explain in detail how to manage your Particle Assembler ads in this article about our Ad Manager. However, there's an important distinction to be made for Facebook Instant Articles.
In Particle Assembler posts, you can choose the frequency of ad breaks for your ads, and whether you want to make that decision per post or globally (this is all explained here).
But when it comes to Instant Articles, we don't support ad breaks that've been globally set up for the Particle Assembler (meaning ad breaks that have been set up from within the Layout & Design tool).
So bear in mind that you'll have to consciously make the decision to set your ad breaks every time you want to publish a particular Particle Assembler post to Instant Articles.
In short: If you want ads to be displayed for Instant Articles, you need to set the ad breaks in the Entry Editor per post — not globally.