There are 3 hotels on the monorail system and they are all located next to the Magic Kingdom: the Contemporary, Polynesian and Grand Floridian.
You are right, the monorail system services EPCOT and Magic Kingdom.
To take the monorail from one of the 3 monorail hotels, you would need to disembark at the ticket and transportation center (between Poly and Contemporary) then get on the EPCOT monorail.