How does one differentiate between desserts that are considered a separate course and those that are eaten as part of the meal (i.e. a more informal meal). Additionally, what is the Halacha of making a Bracha on fruit at a meal? Is there a difference if it is an appetizer or part of the meal itself?

There are many details to your question and I can’t go into all the detailed cases. (See V'zot Habracha Capter 8 for all details) In general, food that does not come as part of the meal (or an appetizer) and is eaten as an addition (before or after) to the main meal (e.g. fruit desert) will require its own Brachah (cake is different since it is covered by Hamotzi in most cases).