Experience. We were on a Pendolino last time we travelled with Virgin, so it may not be exactly the same, however, do ask the platform staff where they want you, so you can load the bikes without too much fuss, and remind the train manager that he/she will need to let your bikes out at the other end, and it should be fine. (IIRC, the reservation system will give them a reminder at your destination too). Remember that you can't get back to the bikes 'til after the journey, so make sure everything you want is in the bag you take into the train with you!
On the Pendolinos, the part the bikes travel in is right at the end of the train (as they come in to Crewe). Both Crewe and Piccadilly have a "Cycle Boarding Point" sign, as I recall, indicating where you should be.
Depending on when I arrive at the station, I've travelled with the other companies as part of my commute, I try to avoid Cross Country though, as the LHT is a bit of a heavy bike to be hoisting onto a wheel hook.
