Сам делаю так,
грубый пример //Вход
var claims = new List<Claim>();
claims.Add(new Claim(ClaimTypes.Name, "Brock"));
claims.Add(new Claim(ClaimTypes.Email, "brockallen@gmail.com"));
var id = new ClaimsIdentity(claims,DefaultAuthenticationTypes.ApplicationCookie);
var ctx = Request.GetOwinContext();
var authenticationManager = ctx.Authentication;
authenticationManager.SignIn(id);
//Выход
var ctx = Request.GetOwinContext();
var authenticationManager = ctx.Authentication;
authenticationManager.SignOut();
