Bob...there is nothing wrong with your idea to use the NP-2DD "over and under dots" as you state! Try it, and if it works for you, fine. However, like the other responders to your question, I would not bother to use it; rather, just click up/down the elevation going from 600 to 1,000 yards.
There is one exception though where I regularly use the lower dot! That is for 1,200 yard shooting...a fad at the Midwest Palma Championships held annually up at Lodi, WI. Here I fully employ your idea. Following the 1,000 yard match, I click up 2-3 minutes of elevation depending on the load being used for my 7mm RSAUM, go to 42 power, and use the "lower" dot. For me, the lower (and smaller diameter dot) at 42 power provides a pref errable aiming dot for the much diminished size/appearance of the 1,000 yard target face (conditions permitting). In this instance, I'm really not too lazy to just "click up", I'm after "uncovering" the 10/X rings as much as possible as they are obscured by the larger upper dot, by using the smaller aiming dot, and to more better hold on on the rings horizontally for windage purposes.
Danny Biggs