We booked with A company named Culturas Peru. They took care of everything...in country travel, lodging, passes to machu picchu, all our meals when we were on the trail, and we had a great guide with us the whole time. It cost us about $2200 a person for 9 days, that's not including international flights to get to Lima. A bit pricey for a 3rd world country, but I definitely feel we got our money's worth. Everything went perfectly smoothly, the food was awesome, hotels they booked were very nice, and our guide was great!
You could definitely do it less expensively if you took care of all in country travel and lodging yourself, and just booked with a guide for the inka trail and machu picchu. If I were to go back, that's how I would do it. I usually don't like doing everything through an agency when I travel, but didn't know how it was down there...and was going with my wife. So I wanted to make sure everything was gtg and safe.
Access to the inka trail and machu picchu is strictly controlled by the government. 400 people a day are allowed to enter the inka trail a day, 1,000 allowed to enter machu picchu (including the 400 from the trail). That's hikers, guides, porters, everyone. So you have to book a while in advance. And from what our guide was saying, they are just going to restrict access more and more, and even close off certain areas completely. So get there soon....it's probably the best trip I have ever taken