You haven't explained: Do you prepay when you book through the conference site, or do you pay at the hotel? If you prepay, you are right, you won't get 5x points on the Marriot Chase card, because it'll come through as a charge to the conference site, not to a Marriott hotel. If the conference site does not take prepayment, but simply books the hotel for you (takes your credit card number but simply forwards it to the hotel), you'll still be paying the hotel (just at a conference rate), and the Marriott Chase points will still be 5x.

If you haven't yet, you need to look carefully at the booking rules on the conference site to determine who bills your card when.