There are quite a number of good hotels in Bordeaux and we've used in the past both the Continental Hotel (doubles : 85 or 104 Euros) which is centrally located (we're giving these addresses without sponsorship...), and the very cheap Hotel Formule 1 chain (34 Euros a room, breakfast included - all rooms can accomodate for this price 1, 2 or 3 people), which is located on the other side of the Garonne (see map), at a 15 mn walking distance from downtown (plus, they have a parking lot). You can reserve your Hotel F1 room through the internet (they're very basic but good value and fill up fast, so do it early).
We'll skip the Bordeaux visit this time and concentrate on St-Emilion which is a good base to visit the region.
In spite of having all the features of a wine-tourist trap (like Beaune in Burgundy), with its collection of luxury wine shops and well-polished old streets, Saint Emilion is still a lovely place from which you can plan your exploration of the Bordeaux region without being bothered by the traffic. Once in Saint-Emilion, try not to loose your time with window shopping on wine paraphernalia that you'd probably find anywhere in the world, and start your time travel in this lovely small town...
Saint-Emilion is an extremely-well preserved village and walking along its streets is a pleasure. As it is sitting at the top of a hill, you have several spots with nice views over the town's roofs and the vineyards, like from the Place du Clocher near the Tourism Office. This "Office du Tourisme" provides the visitors with lots of info about the town and the wineries. St Emilion is literally encircled by vineyards, and some of the estates around St-Emilion were first planted by the Romans. The Roman Poet ausone for example, owned one of the three properties of his time, including what has become Chateau Ausone. I can't but recommend an excellent guide book to vist the area, it is Hubrecht Duijker's Touring in Wine Country, Bordeaux (a collection directed by Hugh Johnson). The French edition seems to be sold out but you should find the English version. Its many maps covering each of Bordeaux Appellations are so detailed that you can easily find the properties yourself, and these maps will also be of great help to understand the Appellations and locate the estates and their neighboors. Many world-renowned estates are at an easy walking distance of the village, like Chateau Ausone, Chateau Bel Air, Clos Fourtet, Chateau Canon or Chateau Beauséjour Duffau. Take the right street and path, and you can be walking along Ausone's vineyards or Chateau Canon's in the matter of 5 minutes after leaving the Place du Clocher.
Another good option to explore thearea is to rent a bicycle. You can ask at the Tourist office near the Place du Clocher, according to this page, they have bicycles to rent. The Chambre d'Hôte where you stay may also have a few bicycles for your own use (like the Chambre d'Hôte of Chateau Meylet), and that may be one of the things to ask before choosing your accomodation. You can also join of of these costly packages where your bicycle tour is organized through several points of interest and estates, like here. If you are an experienced cyclist and feel that you can travel on your own bicycle like this fellow on left, prepare your gear (don't forget the rain coat) and take the road from Bordeaux, your trip will be very rewarding especially if you keep using the small roads. See this page for a few tips.
In St Emilion proper, you still find authentic streets and places if you venture out of the beaten path. It is a good surprise to see these simple scenes, untouched by the wine & luxury culture. We walked along this "rue des Douves" [pic on left] as we came back from our stroll near Chateau Canon and Chateau Ausone. Very quiet walk, we were basically alone. I noticed the many fig trees in the area and must confess that I picked a small branch from a fig tree on Ausone property, with the goal to have it grow in the Loire. I'm not sure it will work yet, I'll keep you informed. Whatever, we came back to St Emilion through this narrow street bordered with many unused caves and underground galleries, some of them being walled. These galleries were initially quarries, not cellars. A nice smell of freshness and cold rock cellar came to us as we walk along this quiet path. See this page for a detailed plan of Saint Emilion.