If you are having the true full flexi account, it works very simple.

You just need to dump in the amount of money into your account that is same to the amount bank pay to developer, then no interest charge shall incur. Depending on the bank, there may have some additional maintenance charges (RM 10 per month for example).

Let say bank pay RM 50k to the developer, and you put RM 50k into the account, then you do not need to serve any interest.

If let say bank pay RM 50k to the developer while you only put RM 20k into the account, RM 30k will be subject to interest and will be automatically deducted from the RM 20k you put in.

There is no need to start the installment officially with the bank early, you can just every month put in the installment amount by yourself into your flexi account and definately it will reduce the interest.   

The principle for full flexi account is simple and straightforward, they only charge interest on the outstanding amount. The higher outstanding you have, the higher interest you need to pay.