Currently, TurboTax does not support filing an 8889 for each HSA that you have.
However, the IRS instructions on page 10 in Pub 969 state:
"If, during the tax year, you are the beneficiary of two or more HSAs or you are a beneficiary of an HSA and you have your own HSA, you must complete a separate Form 8889 for each HSA. Enter “statement” at the top of each Form 8889 and complete the form as instructed. Next, complete a controlling Form 8889 combining the amounts shown on each of the statement Forms 8889. Attach the statements to your tax return after the controlling Form 8889."
You can crate this "controlling" 8889 by thinking of your two HSAs as a "virtual HSA". You have to do this anyway, because the sum of your contribution cannot exceed your annual HSA contribution limit.
So just enter data in the HSA interview, as if you had one mega-HSA.
P.S., in previous years, I assume that you entered contributions to your HSA as "personal" or "direct" contributions (i.e., no through your employer). You can still do that on the screen headed by "Let's enter [name]'s HSA contributions" on the second line (personal or direct).
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