According to the Shulhan 'Arukh, Habdalah is made on a cup of wine at the conclusion of Yom Kippur, but there is no blessing on Besamim (spices), even if Yom Kippur falls on Shabbath. The Mishnah Berurah comments that many Aharonim disagreed with the Shulhan 'Arukh.
In Rab Pe'alim, Hakham Yosef Hayyim, 'a"h, writes that since many are of the opinion that one should recite the blessing of Besamim, it would appear that it is preferable to recite the blessing on the wine and then afterwards recite the blessing on the Besamim.
Since, however, those who say not to recite the blessing, include such important sources such as the Rambam, the Kolbo and the Shulhan 'Arukh, and that, according to them it would constitute a Hefseq (interruption), he adds that it is good to be concerned about their opinion. Therefore, one should recite the blessing of Besamim on the spices, after concluding the Habdalah.
(See Shulhan 'Arukh, 624:3. Mishnah Berurah, ibid., 5. Rab Pe'alim 3:38)
havdalah Motzei yom kippur, Habdalah Mosei Yom Kippur, Besamim