Though Set and Type are different in Coq, this is mostly due to historical reasons. Nowadays, most developments do not rely on Set being different from Type. In particular, Adam's comment would also make sense if you replace Set by Type everywhere. The main point is that, when you want to define a datatype that you can compute with during execution (e.g. a number), you want to put it in Set or Type rather than Prop. This is because things that live in Prop are erased when you extract programs from Coq, so something defined in Prop would end up not computing anything.
As for your second question: Set is something that lives in Type, but not in Set, as the following snippet shows.
Check Set : Type. (* This works *)
Fail Check Set : Set.
(* The command has indeed failed with message: *)
(* The term "Set" has type "Type" while it is expected to have type *)
(* "Set" (universe inconsistency: Cannot enforce Set+1 <= Set). *)
This restriction is in place to prevent paradoxes in the theory. This is pretty much the only difference you see between Set and Type by default. You can also make them more different by invoking Coq with the -impredicative-set option:
(* Needs -impredicative-set; otherwise, the first line will also fail.*)
Check (forall A : Set, A -> A) : Set.
Universe u.
Fail Check (forall A : Type@{u}, A -> A) : Type@{u}.
(* The command has indeed failed with message: *)
(* The term "forall A : Type, A -> A" has type "Type@{u+1}" *)
(* while it is expected to have type "Type@{u}" (universe inconsistency: Cannot enforce *)
(* u < u because u = u). *)
Note that I had to add the Universe u. declaration to force the two occurrences of Type to be at the same level. Without this declaration, Coq would silently put the two Types at different universe levels, and the command would be accepted. (This would not mean that Type would have the same behavior as Set in this example, since Type@{u} and Type@{v} are different things when u and v are different!)
If you're wondering why this feature is useful, it is not by chance. The overwhelming majority of Coq developments does not rely on it. It is turned off by default because it is incompatible with a few axioms that are generally considered more useful in Coq developments, such as the strong law of the excluded middle:
forall A : Prop, {A} + {~ A}
With -impredicative-set turned on, this axiom yields a paradox, while it is safe to use by default.