Hi there, I apologize for being late on this.

D'Altroy's "The Incas" (Blackwell, 2002) is still a solid resource for generally understanding the Incas, and I also like Gordon McEwan's more recent volume, "The Incas: New Perspectives" (ABC-CLIO, 2006). (EDIT: There's also an even more recent volume with a lot of pictures, by Craig Morris and Adriana von Hagen, "The Incas" (2012, in Thames and Hudson's "Ancient Peoples and Places" series). Also, a friend reminded me that D'Altroy put out a new edition of his volume which updates the book with new research from the last decade.)

If you're looking for a more historical treatment, especially of the precipitous rise and fall of Tawantinsuyu at the hands of the Spanish (and indigenous groups!), I would suggest two volumes: one is John Hemming's "Conquest of the Incas" (originally published 1970, with a more recent edition from 2003?) and Kim MacQuarrie's "The Last Days of the Incas" (Simon & Schuster, 2008). Both are very well sourced with connections to the archaeology as well as the history of Inca Peru.

Finally, with regard to the archaeology of only Machu Picchu, I would highly recommend Richard Burger's "Machu Picchu: Unveiling the Mystery of the Incas". When Hiram Bingham "discovered" Machu Picchu (led there by the ten year old son of the farmer who owned the land...) he conducted a lot of archaeology there - and took the artifacts back to the Peabody Museum, where they stayed for nearly a century. This became a hot-button issue between Yale University and the Peruvian government, who wanted the artifacts back for the centennial of the "discovery" of MP. So Richard Burger and his wife/fellow Yale researcher Lucy Salazar worked on the collection of artifacts at the Peabody, put out volumes and articles like this, and then got the material back to the Peruvians (yay!). You can visit and view this collection at the Museo Machu Picchu in the Casa Concha, which is a half-block or so east from the northeast corner of the Plaza de Armas (central plaza) of Cuzco (which I assume you'll be visiting for a time if you're taking the Inca Trail). What's incredible about the Machu Picchu collection is that it represents artifacts of the Inca royalty, often made of silver and gold, which did not otherwise survive the Conquest's lust for precious metals. The only examples of Inca silverware come from that collection, among other things. Also, it should be noted that while Machu Picchu has a Sun Temple and Moon Temple in it, this was not a monastery: it was a royal estate, a retreat for Pachacuti Inca during the cold winter months up in Cuzco. Of course, as the Son of the Sun he had to keep "keyed into" religious rites and timings, but this was a place to rest, to plan and work with fellow elites, to hunt for sport. Burger and Salazar are probably some of the best resources to understand Machu Picchu as archaeologists understand it, far beyond the recent New Wave focus on "spiritual energies" of the site which appear to focus everyone's attention to the Intihuatana of the Sun Temple to the exclusion of the other fascinating parts of the estate.

Also, if you'd like I can make plenty of other suggestions for archaeological sites to visit in the Cusco region, or wherever else you're planning on going while you're there.