I am in the same boat and posted a question just now (was not able to search this). As mentioned in the thread, imports from both Marcus and Ally are wrong.
What I ended up doing was to enter multiple 1099-INT with Bank name as Ally Bank Account XXXXXXXXX.
Reading on IRS site, it seems if you have multiple accounts at a bank, you should specify the account number with each. See instructions at IRS (click on Account Number on left navigation menu).
Although in past I have just combined them into one. So I believe either way should be fine.
