It takes only 20 mins from the Kota Kinabalu jetty to the island. I must say it's a very bumpy ride.
You can buy the tickets at the counter office at the jetty. The price of the ticket is pretty reasonable.
Do take note that the boat doesn't leave the jetty based on any schedules, however, it will leave when there is at least a min of 6 persons who are going to the same island. The same applies when you're heading back to the jetty at Kota Kinabalu.
Just fyi, you can do island hopping as well, and of course the price will be slightly higher. But keep in mind that it will be very inconvenient to do it unless you're with a group of at least 6 persons and above, who wanted to hop to the same islands as you do and come to an agreement on the time of when to depart from one island to another, otherwise you'll have to wait a long time...
Your travel agent will most likely pick you up from hotel, bring you to a pier for boat transfer to Manukan Island
The only way to get to Pulau Manukan is by speed boat from Kota Kinabalu. It takes about 20-30 minutes to reach the island.