Do you mean that you have two separate 1099-B forms, one for you and one for your wife, from the same brokerage? You can enter more than one 1099-B from the same brokerage. To help keep them straight, on the screen where you enter the name of the brokerage, enter the account number.
After you finish entering the first 1099-B there are several summary screens. When you get to the one that says "Here's all the investment accounts we have so far," click "Add More Sales." That will start over at the beginning and you can enter the same brokerage name and a different account number.
TurboTax does not ask you who is the owner of each account, and does not keep track of who the owner is.