1. You received two 1099-SA forms. This is correct. The 1099-SA with code '1' was for any 2017 distributions you made (i.e., paid for medical expenses). The 1099-SA with code "2' was to report the withdrawal of the excess for year 2016 and to report any earnings that this excess made while in the HSA.
NOTE: the excess for 2016 was added back to your income in 2016 so you are done with that. The earnings, however, could not be reported until during tax year 2017 (because the time that the excess was in the HSA spanned 2016-2017). So only the earnings from the 1099-SA with code '2' will be added to your income in tax year 2017.
2. I do not know what you mean by "two submissions", but if you mean that you entered both 1099-SA forms in TurboTax, then this is correct.
3. You answered the question about overfunding correctly. The questions really means to ask, "Did you carry over any excess contributions from 2016?" Since you withdrew the excess for 2016 in early 2017, you "cured" the excess and so did not carry over any excess to 2017.
