MH online website was probably designed in the 90s with no updates. Worse still, they have two different booking systems - on MHMobile and malaysiaairlines.com. If you book on one, your bookings are (sometimes) not visible on the other. Talk about an archaic system! Even if you were to be able to access your booking online, you will not be able to select your seats - this has to be done at time of booking (and only if you booked on the malaysiaairlines.com website) or when you check-in online.
To be honest as the above poster has said, your best bet is to give their customer service helpline a ring. The wait is relatively short and the agents on the phone are generally very helpful - everything from selecting seats, changing the date your fly etc. As you mentioned the booking reference will remain the same, and their website is slow to update, but they should send you an e-mail documenting the change to your itenary.
Had to go through this process, twice yesterday.