When you are at the Ninjas Live Home screen you can find Bank in the left hand column, which is under the Ancestors where you spend Honor Points above the Healer. Once you are in the Ninjas Live Bank you are going to see a relatively simple interface, especially compared to the other MMO text-based iPhone RPGs. At the very top of the Ninjas Live Bank list you will see your Bank Balance listed. Below that you will have a text prompt that you can enter an amount in that you want to deposit.
If it is your first time for using the Ninjas Live Bank it will say "Open Account with" above the text prompt. Right off the bat there will likely be all of your available Ninjas Live Money listed in the Ninjas Live Bank text prompt, so you are going to need to change this if you do not want to deposit all of your Money. There is a ten percent fee put on all incoming money that you deposit into the Ninjas Live Bank, though it is free to withdraw money at any time.