Hi yuujh
The new remote should have automatically paired during the migration process.
Please try the following which should work by holding down the 'Live TV' and '0' button together for around 10/15 seconds. The Standby button should then start to flash followed by an onscreen message displaying 'Pairing successful - this remote will only work with this Virgin 360 box'.
You can also try the following:-
Put the box into 'Pairing Mode' by pressing the Standby/On button on the front of the 360 box for 10 seconds. Then using the remote control, press and hold the 'Live TV' button and the '0' button together for 10/15 seconds. And fingers crossed hopefully a message should appear on the screen confirming that pairing was successful.