If you have used a travel guide, it will contain hotel recommendations. Most have reviews, include pricing or at least pricing categories, for each individual. Many will be able to book online.
But some of the smaller self-owned hotels are still doing themselves. Most you can respond to via email, but some are a little more old-fashioned and only take reservations about the phone. If that is the case, do not let the idea of calling internationally and speaking to someone, as English is not their first tongue, scare you. These are business people who live and provide rooms for tourists who guess what may not speak their native language. They speak all English enough to take a reservation!
Look at your itinerary and start booking these hotels for each location. You generally want to book at least 2-3 months before, just to make sure that you are able to get exactly the hotel you want. If you are traveling in high season, you can start a little earlier. Most hotels require a credit card to reserve the room, but most will allow you to pay cash on arrival.
When these hotels are booked, please write down the contact details (hotel name, address, phone number) and save your records. There is also a great website called Tripit, which has a travel software tool that allows you to either enter this information manually or even has a feature that you can forward them to confirmation email (for hotels and even airline info) and it will actually do it for you.
For my hotel choice I'm in the middle of here. I can not afford to stay in five-star hotels, but I do not want to be disturbed by unpleasant circumstances like a crowded youth hostel. I prefer to have the best of both worlds: experiencing the country, people and culture that I have immersed while I do not stay in "outlined" accommodations. I lean towards small, independent owned hotels, close to the city center, but read from the sites that are choked with tourists.
Plus most of these self-owned small hotels are run by the owners themselves, which are always more than happy to help their guests. They are one of the best travel advisors you will come in while you are there. They can tell you where the best local places to eat, the easiest ways to navigate in the city to help you book museum reservations and tours.