To which extent were the stories and events from the Clash of the Titans (franchise) films based on real Greek mythology and to which degree were they just made up for the movies?
Most of the elements are indeed taken from Greek Mythology however they've been put together in a different manner. I'll try to outline a few changes:
Perseus did indeed kill Medusa and save Andromeda, however in the myth it was a sea monster sent by Poseidon not Hades, it was indeed based around the city of Argos.
Medusa was actually one of three Gorgon sisters (Medusa, Stheno, and Euryale)
Perseus married Andromeda not Io (who was in fact a nymph who seduced Zeus)
Bellerophon rode the Pegasus not Perseus
The Kraken is a sea monster in Norse mythology not Greek
Zeus defeated the Titans by tricking his father Kronos not Hades and the Kraken.
In summary a lot of the elements of the story were taken from various greek myths, many of the characters were very real characters (if you read many of the myths the gods play as central role as the humans - there is no question of their existence). However the stories has been combined in a new way to create a film.
The movies are loosely based on Greek Mythology. There are a lot of faux pas in the movies which makes them fun to watch, but not accurate to the mythology. Here are a couple of sites which explains some of the issues:
Even Hollywood movies based on true events are just "based" on true events. Liberty is almost always taken to tell a better story or make it more exciting, or whatever.