I think this may be the Falcon Quinn series, which starts with Falcon Quinn and the Black Mirror
Thirteen-year-old Falcon Quinn and his neighbors, Max and Megan, board bus number 13 for school on an ordinary day in Cold River, Maine. Only the bus doesn't take its ordinary route, and Falcon and his friends soon find themselves in an extraordinary place—on Shadow Island, at the Academy for Monsters.
With a student body stranger than the cast of any monster movie Falcon has ever seen, the academy is home to creatures and oddities of all kinds. In the academy's atmosphere, Falcon's friends begin to unleash and enjoy their monster natures, from flying with Pearl, La Chupakabra, to decaying with the "Zombie Snap." Falcon has always felt different, with his one bright blue eye and one shadow-black eye, but is he really a monster? Will he discover the other thing that makes him different when he finds himself in the Black Mirror? And when he learns that the school's mission is to teach students to hide their aberrant natures, Falcon and his friends need to find a way to fight back for their monster selves.
I initially thought that the "two hearts" thing might be a description of his dual nature, but no, it's literal.
“Yes,” said Dr. Medulla. “Falcon Quinn has two hearts ”
I have two hearts, Falcon thought. I have always had two hearts.
It looks like it's "Jonny Frankenstein" (all of the Frankenstein's monster constructs are referred to as "Frankensteins") who is his roommate. The TV Tropes page indeed admits that Falcon's father is under a curse and lives in a tower. And he's indeed a bit of an antagonist, being the sort of fanatic who is willing to let others die to attain his cause.
In the second book, Falcon Quinn and the Crimson Vapor:
Falcon Quinn survived the first term at the Academy for Monsters along with his monstrous friends Max, Pearl, Mortia, and the rest. He has finally discovered his monster nature and is working hard to embrace it. But what does it mean to be an Angel, exactly? Having wings is great, when Falcon can remember to use them, but with parents who are the leaders of two warring groups—the monsters and the guardians—Falcon still feels torn in half.
When his monster friends begin to doubt his loyalty to the monster world and his only option is flight to Guardian Island, where his mother rules and he is a prince, he'll see the guardians as well as his monster friends in a whole new light. He will also have to decide if Jonny Frankenstein can be trusted and find a way to save his friend Megan from her imprisonment on Guardian Island, not to mention find a way to stop the monsters and guardians from fighting, once and for all.
Found by browsing the Literature entries on the TV Trope, All Ghoul's School.