We do this journey quite often as DS lives in the Alps.
Dijon is really, really, lovely - it might technically be a city but I think it's more like a large town. Easy to get into & out of & The Hotel Mercure has safe underground parking. Lovely old, pedestrianised centre about 5 mins walk away & parks etc.
We have also stopped in Reims, which is also nice but hell to get in & out of.
Just beyond Troyes, about 20 miles off the motorway is The Lac D'Orient which is also a regional park. We've never stopped there but there are loads of places to stay round the lake & there is swimming etc. Might be a nice break for your DCs.
Chalon sur Saone is half way between Calais & Geneva - DH worked it out exactly 
Whatever you decide I would say to book asap - France gets jammed in August.
Logis de France have a good website, in English as well as French & some of their hotels have pools & family rooms & you can get a good deal on Dinner, B&B.
The cafes in the autoroute stops are expensive & pretty dire - picnic in an aire is much nicer.
It's a really easy drive, just boring for a great deal of the way.