That's not correct, just because you paid for a year long course, doesn't mean you got a year visa. Most of the cheap Thai language programs can only get 90 day Ed visas. There are 1 year Ed visas, you don't extned a 1 year Ed visa every 90 days, it's already a year VISA.
Sorry, maybe I'm in a mood. Yes, you can apply for an Evisa while in Thailand. Being on a current visa wouldn't effect anything, people transition from one type to another all the time.