Travelling overland is a great way to see a place. There are lots of companies that combine your security with off-the-beaten track adventures. You'll get up close and personal with a country's citizens, see sights that are off the tourist trail and get involved in local customs and activities.
You'll also get the chance to stay in a wide variety of places, from sleeping under the stars to being invited into someone's home.
If you choose to go it alone, and you're on a commonly-travelled backpacker trail, it should be easy to arrange various legs of your journey. Often, your hotel, hostel or guest house will book things for you. Asking other travellers what they've done and what they recommend is a useful way of deciding what to do, especially if they're travelling in the opposite direction from you.