I agree with Kupa, just show up in Kota Kinabula and walk into several of the dives shops, the cheapest you will find will be for about US$100 a day, you might want to email some of these places first, as mentioned above, you could get there and they might be alll booked up. Use
www.airasia.com for getting to KK, be advised 15kg. max, I just paid them a fare chunck of change last week to get from KL to Bangkok, they could care less about 'dive gear', but there prices are cheap!
Manado, was just there in July, 4th-11th, check out
www.bunakendivers.com, nothing special but good people, Terry Bradford an Aussie who runs the place is a great guy and very guest orientated, I stayed in their dive lodge for US$10 a night, simple with only a fan and outside bathroom, but this included 3 meals a day. Diving is about US$50 for two dives and a bit more for distant trips. Hands down, diving in Manado rivals Sipadan in many ways, I have now been to Manado 3 times and I will go back again. Hope this helps out. By the way, I flew with Silk airlines from Singapore, found a good deal through "Chanbrothers" a agency out of Singapore.