We've done it both ways, and there advantages and disadvantages for either.
But if it's for next year, you have time to make your booking. Personally, I'd go for a longer ferry trip and book an overnight one. And book a Commodore Class cabin (Brittany Ferries) or their equivalent - rather than just a cabin you get more of a suite, which means that once the DC are asleep you and DH can have somewhere more sensible to sit. They also have a double bed rather than you and DH having to sleep in bunk beds.
The DC always used to enjoy the ferry - it's exciting sleeping somewhere different - but you need to book them very early as the cabins get booked up very, very quickly. What happens is that everyone who knows they're going to France will book their ferry first, and then sort out their accommodation - so if you leave it too long, they will all be booked up.
The other thing I would recommend is that you search out a good hotel en route - which doesn't necessarily mean expensive in France - and find one with a swimming pool. Have a look at the Michelin red book.
Pack a separate overnight bag which is easily accessible in the car, and then you don't have to unpack the whole car.
I love, love, love holidays like this and I want to come with you!