We did not take any formal tours in Peru however I'll give you some good basic information. I'm also in the process of putting together a small packet of information for other people who requested it which I'll be glad to mail to you.
Cuzco/Machu Pichu: We set up our airfare and lodgings with a package through Colorama Tours(check with your travel agent)
We stayed in a four star hotel, the Picoaga which was about $43 a night for a double. There are other better deals and if you arrive in Cuzco without Reservations there are reservation desks at the airport. Also cab drivers will barter with you to get you to town and get you a room. They can get you good deals(during our second stay in Cuzco we didi this and stayed at the Colonial Palace for $25.00).
The nice thing about having a tour arranged is that they will offer you day trips if you like that sort of travel. They will also deal with your airline. Flights must be confirmed and reconfirmed and you must arrive one hour early or your seat will be sold.
You have two choices for getting to Machu Pichu. Most people take the Tourist Train(Auto Vagon) which costs $60.00 round trip. This takes about 3 hours and is very plush and icnludes an informational movie about the ruins, your bus fee up the hill from the train ($7.00), your entrance fee to Machu Pichu ($12.00) and a full lunch (Supposedly worth $14.00 and you'll end up paying at least $5.00 if you buy a la carte.) Your other option is to take the local train which takes 6 hours and only costs about $5.00 each way. What's nice about his is that you get a real local flavor and the local indians come on board and sell food (not just small snacks -- we're talking about corn on the cob, Stews, fresh fruit, roasted pigs etc.). This is really a once in a life time experience. However Do not take the local train back to Cuzco because you cannot reserve a seat. And you will be forced to stand in the aisle dodging the food hawkers who were so much fun to see on the way up. It's very unpleasant. You can buy a ticket on the Auto Vagon to return. Actually, you may not want to take a train all the way back to Cuzco as there are many great ruins between Machu Piccu and Cuzco (the Sacred valley).
Before we left Cuzco We had pre-arranged a tour with a local cabby/tour guide who met us at Ollatantambo and took us through the valley at our own pace. There are many tourist offices along the Plaza De Armas in Cuzco and they are all able to arrange these (We used Jorge in the Hotel Chaska and were very happy with his work).
If you wish to stay overnight in Machu Pichu (which you should do -- otherwise you only get a few hours at the ruins) you have two choices. There is a tourist hotel on Machu Pichu which has about 20 rooms but is very expensive and the food is overpriced and bland (on the other hand, like they say"location, location, location"). We stayed in Aguas Callientes which is the nearby town at the foot of the mountain (a 10 minute walk to the bus stop). There are pleanty of dirt cheap backpacker style hotels in town and they generally do not require reservations. We stayed at the brand new Machu Pichu Pueblo hotel. This is run by an experienced chain and is incredibly beautiful and at $40-$50 a night is a great deal ( In the U.S. this would be a $200 a night hotel). The food was $10.00 prix fix and was delicious. And the Pisco Sours were among the best we had in Peru.
Amazon/Jungle - We did not stay in the Amazon Proper. There are two general jungle areas. Iquitios is the city that leads to the actual Amazon and there are several Lodges which you can make reservations from there. The problem is that the lodges here tend to be very touristy and there are no animals to be seen.
We stayed in the Tamboppata reserve which is onthe river of the same name this is a southern triubutary of the amazon. The port city there is Puerto Maldonado. We took a three hour boat rdie to the Explorers Inn. This is a rustic bare bones facility with professional naturalist who also do the guiding. They have world record numbers of Butterflies, Ants, Monkeys and birds. I t' s a prety rugged palce but he food is good the accomadations are clean and comnfortable. There is no electricity because the generators scare off the animals. The jungle is very interesting and the guests and guides were good people. You can arrange your trip there through travel agents here or in Lima at their office. People have also been known to drop in from Puerto Maldonado.
Other lodges in the area that are more plush include the Tambo lodge and the Jungle lodge. but you wil be hard pressed to see any animals.
I strongly recommend that you read the Lonely Planet guide to Peru becaue he has some good recommdations.
General notes:In Cuzco you may very well get altitude sickness on your first day so you should plan on staying at least 2 nights (drink the Coca tea it helps).
Cab drivers do more than drive cabs. They arrange tours etc. They are vey useful and mostly legitimate.
Money-Travelers cheques are very hard to exchange and only American Express will work. Take as much cash as you are comforatable with. or expect to stand in long bank lines and to not be able to exchange in every city.
Cambiaristas are money changers who stand in front of banks and exhchange shops. They seem like black marketeers but they are completely legal and give a significantly better exchange rate(2.16 soles to the dollar as opposed to 2.10 in banks). They ONLY take cash.
Air Travel- the easiest wayto get fromn city to city is air travel and you can arrange those flights through you travel agent. Aero Peru is cheaper but they are very unpredicatable and disorganized so be prepared for delayed and cancelled flights.
