I admit, I'm not an experienced enough RTS player to make any real recommendations. However, from what I've seen, Dragon Commander relies not so much on base building (which makes the turtler in me very sad), but on quickly capturing specific points on the map.
So I really wouldn't mind if, on lower difficulties, your troops capture points a bit faster than the AI does.
And while I wouldn't go full sub-commander, it could be an idea that you can issue a general directive somehow (capture points; build unit type X; attack enemy; whatever) that the AI will take care of whenever you launch into Dragon mode to do some more personal damage.
If all else fails, however, there's still the autoresolve button.