If I remember correctly, the times I have used a deposited free-night e-cert, they were removed from my account when the reservation was made and they were attached to the reservation.

So if you are still seeing the certs sitting "unused" in your account, I might call back and ask another agent just to verify.

Another telling sign is that the times I have used my Cat. 1-5 Visa e-certs (at least for the times when it wasn't a Cat. 5 hotel), the online reservation stated that there was a cert mis-match. I assumed this was because the cert was usable for a Cat 5 (and anything less), and I wasn't using it for a Cat. 5 hotel. So if you have a similar situation and see that note, it probably means your e-certs are applied. If you don't, then who knows.

[Edited to add]
I just checked and I actually have a 2-room/1-night reservation for a Cat. 3 RI (I'm heading to the UT/Ark game in November.) I do believe I used points for 1 room and my Cat. 1-5 ecert for the other. The reservation shows at 30K points total cost, but I only see a 15K deduction from my account.

So your reservation may very well be in order. It looks like Marriott's reservation system shows the points that the award would have cost. But if you haven't had the points deducted from your account and the reservation doesn't say something about not having award certs applied (i.e. you see the "if you don't order the needed awards, Marriott will deduct the needed points automatically 7 days before the stay" verbiage), then I suspect your reservation is good to go.

Note I also see at the top of the reservation page the "The certificates attached to this reservation may not match the number of days, room type, or other features of your stay. Please call Guest Services to ensure you have the proper certificates for your reservation" verbiage. But as far as I can tell, my reservation is in order.