My first mistake was booking a single room. While extremely private and comfortable, it dramatically inflates your living costs. For my first 30 days, I paid over $9 per day, just to have a single room. It did not seem like a lot, until I realized a mixed dorm at the same guesthouse cost roughly half the price. Unless a single room is extremely important to you, or you are traveling with someone (hence, being able to split the cost of a room), I'd recommend going for the mixed dorms. Not only is it way cheaper, you will also meet more people using this method. It's easy to sit in your room alone all day, but dorms force you to meet other cool travelers. Most guesthouses even offer some sort of locker to stash your valuable belongings!
It took me a while to realize that Booking.com is not the only site for booking hostels. In fact, it is rarely the cheapest site. Up until now, I had been booking stays only through Booking.com. My current guesthouse in Siem Reap, Cambodia cost $5 per night. Turns out if you go to Hostelworld.com, there's a hostel available for only $2 per night! If you are booking in advance, browse multiple websites. Some of these include: Booking.com, Hostebookers.com and Hostelworld.com. You can even head to Hostelz.com, which searches multiple booking companies and gives you the best deal. However, I have found that it is not always up to date with the cheapest rates. Search at least three or four different websites; you will be surprised that what is advertised on one, is not always available on the others.
If you are adventurous and have time to burn, you may want to simply skip booking websites. It is generally cheaper to book directly at a guesthouse, and you can sometimes haggle the price down. One of my cheapest island stays in Thailand came from booking a bungalow in person (albeit we split the cost between three people). Downsides to this method do exist. Booking websites have user reviews, so you can find a highly-rated place without worrying about "surprises." You may also miss out on an affordable gem if it's off the beaten path.
While it may only seem like a few dollars at first, saving on accommodation is VERY important for budget traveling. This stuff adds up fast. If you save $2-3 per night during a six-month trip, you'll have an extra $300-600. That's potentially an entire month of travel in Southeast Asia! It's definitely worth it to take the extra time, especially if you have lots of it.