Yes you can do this. Just be aware that they have had some problems with the flight info not getting transferred from the reservations system to the ME system for those people who book room-only reservations. In our case, we provided our flight info to the reservations people but when our confirmation letter arrived, it didn't show we had signed up for ME. I called the ME people directly and they did not have our info in their system, so they added us in manually. I know this has also happened to others who booked a room-only reservation around that same time and I'm not sure if it has been fixed yet.
So, yes you can do this, but follow up directly with ME a week or so after providing your flight info to CRO to be sure ME has received it.
