As far as your tax return is concerned, you have one virtual HSA account, even if you may have several physical accounts. This means that for purposes of the annual contribution limit, the sum of all contributions to all your HSAs has to be less than or equal to the single annual contribution limit.
This means that as you go through the HSA interview, you answer the questions as if the two HSAs were a single account. Enter your contributions no matter which physical account they were for, and enter as many 1099-SA forms as you have.
There is no need to enter data as if you had two separate HSAs.