We had trouble with this last year - we booked through TCD (also Virgin) and the flight website wouldn't accept by booking number. I phoned TCD and they gave me the flight reference. I logged back on and reserved seats straight away.
Please be aware that even though you book the seats for your return trip, unless you confirm them 24 hours before the flight home they will give them to someone else!!! This happened to us even though we did the DTD check in at 7:00am!!!!