Marseille, like a lot of French cities, is broken up by districts called arrondissements, which can be handy in giving a broad location to your hotel if you’re unsure. In general terms, the smaller the number the closer you are to the city centre and Vieux Port - 1ere is the city centre, while 2eme refers broadly to the old town to the north of the Port and the 7eme to the area to the south.
Most of the hotels will be located in these areas, so beware if you find yourself stuck out in the 9eme or 16eme - these are pretty far away from the action and could rack up the travel costs. The main tourist chains (Etap, Best Western, Novotel, etc) are to be found in the city, around the Vieux Port and city centre.
The Tourist Office has an online booking system on their website, with up-to-date accommodation information - http://hotels.marseille-tourisme.com/en/accommodation