It is possible to make your own way from BSB to Kota Kinabalu in a day.
From the main bus terminal in BSB, catch the express bus that leaves at around 7.15am bound for Muara which is the port and customs town for Brunei. The bus will cost you BD2.
At Muara, purchase a ticket for Labuan, which is the port and customs town for Sabah. The ticket will cost BD15 and the ride will take one hour. A departure tax of BD2 is also payable before boarding.
Upon arrival at Labuan, after passing through customs, purchase your boat ticket for Kota Kinabalu which is MYR34 and the trip is about 3 hours.
While waiting for your boat to depart, there is a baggage check in area where you can store your bags instead of carrying them all around with you - a large back pack will cost MYR3 per pack.
You will arrive in Kota Kinabalu at approx 4pm.
To ensure that you can make the trip in a day, you must catch the first boat out of Muara!