What is the best site to book flights and hotels for travel in Asia / Indonesia?

Google is.

I remember hearing ctrip or elong website can help you book flights and hotels to China, not sure about Indonesia..

send us an enquiry: info@xpatstravel.com, we focus on a lot on South East Asia, with our hands on experience, I think we could find out the good deals for you:)
For Bali, if your dates are flexible, we could also help you arrange a direct flight with Shanghai Airline. For Thailand or Langkawi, we have great deals for Feb and March. I hope this is helpful for you.