If you are going with a tour, the operator will help you from A to Z, from transfer transportation, accommodation, food to activities. But if you are an independent traveller, you will take care of yourself and of course it will be hard, particularly when it is your first time in Halong Bay.
Then if you are going by your own, what can you do?
You can make your own way to Bai Chay area in Halong City from Hanoi by bus and then arrange a taxi or motorbike taxi to the Bai Chay harbor and buy a day boat or overnight boat ticket to Halong Bay or to Cat Ba Island. (Halong cruises or junk boats nowadays usually depart from 1 of the 3 harbor: Tuan Chau harbor, Hon Gai harbor and Bai Chay harbor. While Tuan Chau and Hon Gai accomodate 3*-up cruises those require pre-booking, Bai Chay is where you can find cheap junk cruises that you can buy ticket instantly to go to the bay)
You can stop at the Halong Bay Tourist Information Centre at Bai Chay harbor for information and then negotiate price with boat companies (ticket for bay visit has fixed price but price for boat is variable that you can bargain down, but this is not an easy job even for Vietnamese as boat companies at Bai Chay harbor usually agree secretly on price levels).
