My bees have both the regular entrance below the deep brood nests and an upper hole on top of the highest box. Of the three, one hive is almost exclusively (and has been since it was hived a nearly a year ago) top-entrance users. The other two are more adaptable - the largest one, now three deeps and three mediums (and about to get split) uses both of the entrances almost evenly. And the third one is predomintly "normal" and rarely do I see bees going in the upper entrance hole. And that is stable whether there is brood chamber in the upper or lower deep.
It seems silly to me to haul all the nectar and pollen through the congested brood area, but I guess the bees know what they are doing. I see no problem having both entrances available to them and letting them use which ever one they like. The only issue arises during robbing season when I must make sure to have screens on each entrance or screen off the rarely used one on the hive that only uses the lower entrance. To protect the upper entrances on the other two I use small nuc-sized robber screens I get from Betterbee.