On the last screen of the Tax Withholding Estimator, where it shows your refund, click "How to Adjust Your Withholding" to see what to put on your W-4. There is also a slider you can use to adjust the amount of the refund.
The Tax Withholding Estimator doesn't estimate your return. It estimates your refund. Your tax return is the form you send to the government that shows your income and calculates your tax. The money the government sends back to you is your refund.
"His custody situation" has nothing to do with it. Either of you can use either or both of the children on your W-4. It's the same as if they were your own children. The fact that they are stepchildren doesn't matter. On your joint tax return you are both claiming the children together. It makes no difference whose children they are.
