Get your taxes done using TurboTax
Yes, when importing from several accounts at the same institution, the second import overwrites the first one. If you're using TurboTax Online, be sure to clear your Cache and Cookies between imports.
In TurboTax Online, however, you can attach a PDF copy of your 1099-B transactions to your tax file. If you save a PDF of all your 1099's from your institution, you can make a manual entry for the total amounts of 1099-INT/DIV, then attach the PDF for 1099-B's.
Here's more info on Importing Multiple Accounts.
