Funnily enough, although I normally go DIY I have actually used Kuoni once as they came out as cheaply as the price I got for DIY. Dont discount any way of booking. Go through the TOs and TAs. Also price flights on their own. Expedia or Travelsupermarket are good but also price directly with airline. You book flights from Bangkok to Koh Samui with Bangkok Airways.Have to say, the earlier you book these, the cheaper you will get it for. Then you can chose which hotels you really want. As well as price comparison sites, go to the hotel direct. A lot will guarantee to match a cheaper price. For a diy holiday- going to Thailand is easy to do IMO.

I usually go DIY nowadays , I can then pick and mix the Hotels I prefer, having said that I had a few good tailor made packages on my first few visits to Thailand , used Kuoni, Tradewinds, Hayes and Jarvis.

Interesting you should post this, I was about to ask a similar question.

In respect of DIY trips, how is best to sort out transfers etc. Never done this before so would be interested to know people's experiences and which are the best sites to use.

Does it work out significantly cheaper?

Thanks.

If you stay over in Bangkok use the prepaid taxi booth. You say your destination and you pay there and then.
For Koh Samui our hotel picked us up- however, taxis are cheap in any case(well, it has been a few years since I've been so perhaps those who have been recently can confirm or deny this )