Yes I have used and do use the Mark Down manager. And it works wonderfully.
For instance, I have a 75% off clothing sale right now. I listed a group of clothing at the full retail price, then used the Mark down manager to set the 75% off sale for the full 30 days the Store listings run. Super slick.
You can either allow the Mark Down manager to select all of a category. Or you can manually select individual auctions. Just remember. Once you set a sale you cannot add anything else to it. So if you do a jewelry sale for an entire category and list jewelry two days later in the same category, the newly listed jewelry will not be on sale.
And yes, the reduced price is store properly in AW2000.