Not Rouen for the Alps - completely the wrong direction! Reims, as others have said. There's a Novotel in Tinqueux with an outdoor pool and a restaurant. Or the budget option but still en-suite that we usually go for, B&B Hotels chain - family rooms take 4 people and some of them have the kids' beds on a mezzanine above, so it doesn't feel so much as if you are all sleeping in the same room. Pretty good cheap breakfasts too.
If separate rooms is a priority, and you don't mind not having an ensuite bathroom, you could go for the Formula 1 chain and get two rooms for pretty much the price of a family room somewhere more upmarket. The rooms wouldn't have interconnecting doors though, so you might have to be one adult and one child per room. Formula 1 is fine, IME, as long as you are not expecting a 'hotel' kind of experience. Their rooms only take 3, not 4.
Nicer and much more French are Chambres d'Hote which you can find on Booking.com (B&B places, pretty much - usually a room or two in someone's house) but they are rarely as close to the motorway so less good for getting to your destination as quickly as possible - it depends which you want to prioritise. You usually get really amazing breakfasts in Chambre d'hotes, although possibly not until after the local boulangerie has opened for fresh bread and croissants, so not so good for an early get away. We stayed in one last year with a wonderful garden and a trampoline, which was great for kids who'd spent 6 hours in the car. Speaking a bit of French is a help with these, but you can get by with sign language and Google Translate for the initial booking.
Last summer we went from Chalons-en-Champagne (just a bit south of Reims) to Samoens (in the Alps) in a day, so you might not need a second night on the road - only about 5 1/2 hours driving between the two.
Planning the stop-overs is one of my favourite bits of a holiday to France, so apologies for the long answer! Have fun!