I'm planning to travel from the U.k to Indonesia andThailand in October for 6 months and I'm not really sure which travel company to use. Ideally I would like to use one agency to book my flights, hostels and schedule. As it's my first time travelling it's all pretty new to me so any help would be appreciated.
Absolutely no reason why you need a travel agency, and I doubt that any agency would book you with a hostel. If you don't mind a little leg work, travel is not all that difficult these days. Get the help of other travelers and work out a practical itinerary that you can easily follow.
Travelfish.org is the website to seek out for travel to SE Asia - with their experience and knowledge, you'll be able to plan a much better trip than any agency could hope for.
help with Indonesia here
help with Thailand here
Yeah, travel agencies aren't always the best and might actually charge you a bit more than you'd pay on your own. If you're leaving in October you have a lot of work and planning to do in such a short time. If you can you should start buying your tickets soon, waiting until last minute can be expensive...I'd avoid Heathrow if at all possible too...
Daawgon (as usual) provides great advice. Plan to do your own travel planning to save tons of money.