If you use a travel guide, the hotel recommendations will be included. Most have reviews, or include prices, or at least pricing categories, for each. Many will be able to book online.
However, some smaller hotels with independent ownership are still booking their own. Most of what you can match by e-mail, but some are more old-fashioned, and only take bookings over the phone. If this is the case, do not let think of international communication and talk to someone that English may not be their first tongue, and scare you. These are businessmen who earn their living and provide rooms for tourists, guess, and perhaps not speak their mother tongue. They all speak English enough to take a reservation!
Take a look at the itinerary, and start booking these hotels for each location. You generally want to book at least 2-3 months ago, just to make sure you can get exactly the hotel you want. If you travel during peak season, you may want to start a little earlier. Most hotels require a credit card to book the room, but most will allow you to pay cash on arrival.
Once you book these hotels, write down your contact information (hotel name, address, phone number) and save them in your records. There is also a wonderful web site called Tripit, which contains a tool to design a path that allows you to either enter this information manually, or even it has a feature that you can redirect to any confirmation emails (for hotels, even airline information) is yours.
For my hotel options, go halfway here. I can not stay in a five star hotel, but I do not want to bother me with uncomfortable conditions like a busy youth hostel. The best that I get is the best of both worlds: the experience of the country, the people, the culture I am overwhelmed with, while I do not dwell in "obscure" dwellings. I tend towards independently owned small hotels, close to the city center, but protected from areas that are choked with tourists.
In addition, most of these small hotels are run independently by the owners themselves, who are always more than happy to help their guests. They are one of the best travel advisers you will encounter while you are there. They can tell you where the best local places to eat, the easiest way to travel around the city, and even to help you book reservations and tours in museums.