In other words, present the paperwork supporting this division of assets when you sue her for your portion of the money if she has taken some that you feel she did not deserve.
If you are asking whether or not money deposited within your half of the account after the split can be considered as joint assets for the divorce, the answer is "maybe".
Having a legal separation or divorce documents would certainly be helpful because then you would have had a court defining the division. As it is, depending on the state you live in, the court may look at assets you possess at the time of the filing and not consider any arrangement made prior to that time.
I would encourage you to consult local counsel ASAP so that you know what you must do for both of you to be protected.
- Carl