Anthonator on github answered my question here but for posterity's sake this is what he said.
This is what I have in initializers/doorkeeper.rb
resource_owner_from_credentials do |routes|
User.authenticate(params[:username], params[:password])
end
I also have this is my API controller
private
def current_user
@current_user ||= User.find_by_id(doorkeeper_token.resource_owner_id) if doorkeeper_token
end