Hi KingsArmy I've done a mixture of booking transfers direct and booking through hotel. Sometimes the hotel is more expensive, but sometimes it just easier, and Thailand is mainly quite cheap anyway.
We usually book a beach place first so we can get over jet lag and relax, then do a bit more activity for the second part of the holiday. If you're going in the school summer holidays Koh Samui is perfect, so I would plan to fly into Koh Samui, and probably stay at Bophut, know as Fishermans village, it's close to the airport, so I would message the hotel direct and arrange a transfer. Bophut has a lovely clean beach with beanbag bars on the sand and fire shows. There's plenty to do, night markets, restaurants, massages etc. In the past we've done an island tour, last year we did a days boat tour around Ang Thong islands with this company
www.tripadvisor.co.uk/AttractionProductReview-g1179396-d11476114-Angthong_Marine_Park_Semi_Private_Sunset_Tour-Bophut_Ko_Samui_Surat_Thani_Provinc.html
It was a lovely wooden boat, amazing food and they had their own kayaks, so we didn't see another boat all day. There are also speedboat tours there which are about half the price, but they get the kayaks there.
My family all dive so we also headed over to Koh Tao and spent a few days there, it's about 3-4 hours on a ferry, much smaller that Koh Samui, but amazing reefs, really good for snorkelling, we also did a Thai cooking class there.
I would then transfer up to Bangkok or Chiang Mai. Last year we stayed a couple of days in Bangkok and then went to Kanchanaburi. I don't love Bangkok, but it's worth a couple of days, we did a food tour in a tuk tuk visited the huge market and a few temples. Kanchanaburi is very different, Bridge on the River Kwai, so lots of history, stayed in a little eco resort and arranged a trip before we arrived that was quite a long day but really good visiting the railway sites and Erawan falls, a walk that takes in 7 waterfalls. We were going to do it ourselves, but it was so worth getting a guide. We just stayed 2 nights.
We have been to Chiang Mai on a separate holiday and went to an elephant sanctuary, where we looked after them. Also went cycling, and again lovely markets.
Then I'd get flight back to UK from Bangkok, or CM if you can get a direct flight.
Hope that helps!