This is a common trick in pro recording referred to as reamping. Record the guitar direct in, and I am assuming you are using some sort of interface send it back out later at line level into either a passive Direct box or this
http://pro-audio.musiciansfriend.com/product/Radial-Pro-RMP-Passive-Reamping-Direct-Box?sku=153933&src=3WFRWXX&ZYXSEM=0&CAWELAID=26018815
into your pedal and the back into a seperate channel in Cubase. You can make as many seperate tracks as you like and then blend them. You can also do the same type of thing with this setup and various amps, which you would then record with mic(s).
Just to streamline the process you can run an A/B/Y box before the pedal and record A clean and B running through the pedal if you have the ability to record two tracks at the same time. That way if you don't like the settings on the Boss you can record again using the dry channel.

Yikes! I was hoping that Cubase had some setting I wasn't aware of that would allow me to use the GS-10 on an already-recorded track. I don't have any interfaces other than the USB connection from the GS-10 to the computer...

Cubase has the ability to do that, but you'll need an audio interface with multiple ins and outs to route the guitar properly.

So get an two channel interface $200-300. TC Konnect, Firebox, just make certain the one you get is instrument capable, and best to be firewire if your computer is capable.

Antaios wrote: Yikes! I was hoping that Cubase had some setting I wasn't aware of that would allow me to use the GS-10 on an already-recorded track. I don't have any interfaces other than the USB connection from the GS-10 to the computer...

You could turn off everything on the GS-10 so it passes a clean sound with no amp simulation or distortion or effects of any kind. ie; use it just as a USB audio interface. You could then use plug-in amp sims / FX etc.

You can find a list of free overdrive / amp plugs(Dead Link Removed)