Whereabouts do you want to stay? We stayed in a nice small hotel in the middle of Chalon sure Saone, but parking was difficult. We've also stayed in Avallon at the Hotel du Gare (but years ago, so can't say what it is like now). Your main problem, with a smaller non-chain type Bed and Breakfast or hotel, is going to be parking, especially if you have a large outfit. Formule 1, Balladins, Ibis, type chains (of which there are thousands in France) are probably your best bet as they tend to have secured parking areas. There is a web-site for these chain hotels, but at the moment I can't remember it - someone else probably will. It gives you location, etc., as well as price bracket, and you can book through a central reservation desk for most of them.
Have you ruled out an overnight site stop - lots of French towns have very acceptable municipal sites, which are very cheap and usually very central. They tend to open early morning to 'let you out'. I can recommend lots if you want names/locations.