Clamp-o-Tron

I would use the aerodynamics of the atmosphere to your advantage.

That's a Falcon 9 coming through the transonic regime for the landing burn. What you see is the massive angle of attack there- they use the entire rocket like a wing to adjust their landing site, instead of having to do continuous engine burns like you would on a vacuum world to trim your trajectory. Just angle your rocket away from the direction you want to go, and you'll move that way.
To illustrate how this works, even on real life Mars with a fraction of Duna's atmospheric pressure, go watch this simulation of the Mars 2020 EDL earlier today. Notice how the capsule isn't pointed exactly retrograde or towards its target at Jezero Crater? Again, that's using aerodynamics. Scott Manley illustrated something similar here, again. Although both examples are capsules, it works just as well with thinner spacecraft as long as they aren't just atmosphere-penetrating pencils.
Design is less important than you'd think. The stock landers work fine for atmospheric descent and control on Duna, but it would help a lot to add airbrakes. Wings in a lifting-body configuration would greatly assist your crossrange, as said above.
The important part here is pinpointing your trajectory- this atmospheric control can only do so much. Just remember how you would target a landing on a vacuum body, then move that point where your trajectory intersects the ground a specific amount that can only really be obtained with fiddling. Since you know how to make a 10 km accurate landing, I would suggest going back to the conditions before your descent, quicksaving, then iterating the descent until you get it close enough to use aerodynamic control.
Hope this helps!

1. Yes.
2. Yes.
3. Yes.
I currently have 5 installs, some for testing, some for stock gameplay, one for my main modded save. This works from the KSP store, GOG, and Steam. CKAN can handle this easily, there is a button in the top left IIRC to change the which install it's handling.

Anywhere on the vessel will do.