Every day your boyfriend has been incarcerated counts toward his sentence, regardless of where he was held or what stage of the legal process he was in at the time. That time is credit, and it does not disappear because sentencing happened later.
Think of it as money in the bank. From the first day he was taken into custody, the clock started. Whether he sat in county jail waiting for trial, waiting for a plea deal, or waiting for a sentencing date, all of it applies. When the judge imposed the sentence on September 15, 2016, the time already served was factored in or will be credited against the total.
The distinction between straight time and county time depends on where he ends up serving the remainder. If the sentence is short enough to be served locally, he stays in the county. If it exceeds the threshold for state prison in his jurisdiction, typically a year or more, depending on the state, he gets transferred to a state facility. Either way, the pre-sentence credit follows him.
The exact calculation of credit is something his attorney should confirm in writing. Occasionally, there are administrative errors in how time served gets applied, and catching those early matters. If the numbers do not look right once he is processed into whatever facility he lands in, that is a conversation for his lawyer to have with the facility's records office sooner rather than later.