Actually there was only one Dakota territory, not plural as the title suggests. The two states formed out of the one territory in 1889. There was never a North Dakota territory and South Dakota territory but one single Dakota territory that spawned the two states.
Two ideas I can see to have one Dakota
Have settlement more evenly distributed throughout the territory instead of having two population centers in the SE and NE of the Dakota territory. Or having settlement start exclusively in one portion of the state like the Big Sioux river valley in the SE and then spread up to the Red River valley and the Missouri and James rivers.
Having Manitoba as US possession might help as Dakota (North and South) and Manitoba could be the two states admitted.