Простой способ состоит в том, чтобы иметь разные имена для разных полей отправки. Например:
forms.py:
class Login(Form):
...
login = SubmitField('Login')
class Register(Form):
...
register = SubmitField('Register')
views.py:
@main.route('/')
def index():
login_form = Login()
register_form = Register()
if login_form.validate_on_submit() and login_form.login.data:
print "Login form is submitted"
elif register_form.validate_on_submit() and register_form.register.data:
print "Register form is submitted"
...