First let me say that married filing separately is usually the worst way to file so please use the downloaded program so that you can use the married filing joint slash married filing separate breakout so you can see how it is each way before you file and regret it. remember if one person itemizes the other person must itemize even if they have nothing to itemize. also there are other things that are affected by the married filing separately filing status such as credits so be very sure you want to file that way before you do file that way.
Next, how to split the estimated payments. Easy split them any way you want. However if you want to avoid an IRS letter later on then take a look at whose social security number those estimates were paid under. Usually it's the primary taxpayers social security number. For simplicity's sake and not to confuse the IRS, all the estimates should go on that person's tax return. That person should file first and get their refund so they that you have money to pay the balance due on the other person's return.
