Definitely take your own guide book as you will find yourself having to find your own locations for eating in the evening in Amman, the hotel is nice, but just a typical Westernised hotel quite far out from town. It will also help with some of the background to the larger archaeological sites like Jerash and Petra.
Check the itinerary before you go as well, the extra trips our guide had arranged really made a difference to the tour, i.e the National Museum of Jordan to see the new location for the Dead Sea Scrolls, the baptism site on the River Jordan and the extra night in the desert, rather than 3 nights in the Petra Hotel.
Be prepared for a bit of walking in Petra, it is not recommended to use the horses, camels or mules as the owners can be quite aggressive when it comes to payment, walking is certainly manageable as long as you have a reasonable level of fitness.
When changing money, don't be palmed off with an 50 notes. Nobody in Jordan seems to have any change, even in the Amman hotel, amazingly.
Aqaba is seriously hot, (well in June anyway). It was almost unbearable and felt about 10 degrees hotter than anywhere else in Jordan. Also you won't be able to to go on the snorkelling boat trip unless there are enough of you on the trip, we didn't have enough so a few people had to make do with snorkelling off one of the private beaches.