What i do is purchase my flight and then go onto Hotwire/Priceline and book my hotel at a later time. I have found that by doing this I can save money and also if my trip is multi city it can be difficult to do such a package.
For instance in Ahtens I'm paying $66 a Night in a 4 star Hotel via Hotwire and in Rome I'm paying $100 per night also via Hotwire less than a kilometer from Via Venetto and close to Termini/Plazza Republica.
What can happen is Expedia for instance can make it look like your saving but in reality you are paying for the hotel and flight under one transaction. Perhaps you save $100 but is the hotel really good? What I do is first search for the hotel individually and then see what it will cost booked together.
The only real time I did a hotel/air package was when I used a Consolidator(Corsair Nouvelle Frontiers) where for $700 a person you got a hotel and flight(which was a requirement). Not the best hotel.