The major difference between the fundamental fairness doctrine and the incorporation doctrine is that the former is a somewhat vague idea while the latter is much more concrete and specific.
Both of these doctrines have to do with applying the Bill of Rights to the states. The Bill of Rights is supposed to protect our rights from government infringement, but it only applies to the federal government. The Supreme Court has considered different ways to ensure that the states would adhere to the ideas of the Bill of Rights.
The fundamental fairness doctrine was an early way to do this. What it said is that states had to treat criminal defendants in a way that is fundamentally fair. This is not very specific at all. It also means that different states might treat defendants differently. There could be different procedures, but they all had to be “fundamentally fair.”
The incorporation doctrine came later. It was meant to deal with the ambiguity of the fundamental fairness doctrine. It was more specific in that it simply said that the states must follow various parts of the Bill of Rights (practically all of the Bill of Rights is now incorporated). This is somewhat more specific because it lays out exactly what the states must do.