There are a few options. Last year when I went to Sipadan from Bangkok, there were a few options. Basically you will need to fly into Tawau then the resort will pick you up by car to Semporna then transport you by boat to Sipadan/Mabul.
You can fly AirAsia, Malaysian Airline or Royal Brunei. I don't know if there are any changes to flight currently but last year, for Malaysian Airline, I would need to fly BKK-KL-Kota Kinabalu-Tawau with an overnight stay in KL and basically get to Sipadan mid afternoon the next day. AirAsia would be BKK-KL-Tawau but also with overnight in KL and get to Sipadan early afternoon the next day. Royal Brunei would fly BKK-Brunei-KK-Tawau. You wil get to Tawau at about 7pm the same day then you have a choice of getting to Semporna right away and stay overnight there or stay in Tawau and travel to Semporna early the next day. Basically Royal Brunei was the quickest way to get to Sipadan. I am not sure of the schedule now but I think you can fly Malaysian Airline and get from BKK to Tawau on the same day now, I think.
Last year I was also told that Air Asia only allowed 15 kg of check in baggage, otherwise you would have to pay a fine. Don't know if that is true or not.