I'm no pro with Cubase but I have used it a bit for exactly what you are doing. The first thing I would do is check the driver that Cubase is using with your soundcard. For best results with lowest latency factor, you want to be using an ASIO (such as in my case M
Audio Delta Asio) type driver. The next best is a Direct X type driver. These drivers came with my sound card which is an M
Audio Audiophile 2496 (very good card for the money $136). I have virtually no latency with this card. To find out what driver you are using in Cubase go to "Device Setup" then "VST Multitrack".
Also you might want to check that the track you are recording onto is not delayed. Under the "Inspector" there is a place where you can adjust the track delay in milliseconds, you could always go back and adjust this afterward to make your guitar track lineup with the backup.
Hope this helps.
G