Matt,
You do pour the Micro-Restore into the wash at the beginning of the laundry cycle.
Micro-Restore is a detergent, so you want it doing its work to remove all the oils, dirt and car care products from the get go.
The only type of product that you would add durring the rinse cycle is Vinegar (not really need with Micro-Restore, but won't hurt). Vinegar doesn't really do anything to clean the towels, but it lowers the pH of detergents making them more soluble so that they are fully removed from the towels in the rinse cycle.
I have never used the Downey ball, and don't know how it works, so I don't know about that.
I hope this helps. If you have any more questions don't hesitate to ask.
Thanks,
Ian
Autofiber.com