Both versions of the model were used in every production episode of the series.
The model was built for the first pilot in 1964, and was refurbished for the second pilot, and again for the series production. The first refurbishment was mainly changes in painting. Actually, off the top of my head, I forget when the physical changes were made: lowering the bridge dome, the smaller sensor dish, but there were paint detail differences and then for the final refurbishment for the series production, lights were added (which weren't in there at first) and the nacelles were changed then.
The series version is most people's go-to "real" one (with the aft ball structures), at least for the production time period. The earlier versions for Pike and "Where No Man Has Gone Before" tend to identify with the earlier versions of the model.
--Alex