I recently inquired about Havdallah and understand that one says only a blessing on the wine and "HaMavdil BenKodesh Lechol" for ending Yom Tov [dispensing with spices and candle]. What happens when a Shabbat ends but it is during or becoming Yom Tov does one do havdallah - what would be different about the prayers used?

At the end of shabbat chol-hamoed the blessings are identical to those at the end of a regular shabbat. When YomTov begins on Saturday night (motzei shabbat) the havdalla for shabbat is included in the Yom Tov kiddush -check your mahzor or siddur.