Hi
I agree with Clive Francis. The locations mentioned (Koh Samui, Koh Phan Nan, Koh Tao & Chumphon) are located at the Golf of Thailand, which is best suited for diving during the summer months, because it's the monsoon season in the Winter Months.
During the winter months, I'd recommend diving in the Andaman Sea. January is a great month to take a liveaboard to the Similans, Richelieu Rock, the Surin Island, and further north to the Burma banks (Myanmar). Liveaboards leave from either Patong in Phuket or Tab Lamu in Khao Lak. Most of these sites can also be reached from day trips out of Tab Lamu in Khao Lak, which is a developing resort area about 60 -90 minutes up the coast from the Phuket airport. There is also diving (either on liveaboards or land based) in the area surrounding the Koh Phi Phi islands south of Phuket. The Koh Phi Phi islands are stunningly beautiful and offer good diving, however the marine national parks of the Similans etc north of Phuket are far more popular for diving and considered amongst the best in the world.
Thai Airways International offers some reasonably priced flights within Thailand, including packages of several flights.
http://www.thaiair.com/. There is another Thai airline that offers the same thing but I forgot its name.
Keep in mind that if you only have two weeks holiday and want to spend some time in Bangkok, and go on a liveaboard, you wont really have much time to fly around the country (youve got 2 days flying & 12 days holiday, plus post-diving no fly times to think about). I think that youll have plenty to see and do if you stick to the Andaman Sea, and you should consider going to the Golf of Thailand on another trip when the whether will be better.