You should have everything you need already with Cubase. Since you have recorded audio with this setup before you have essentially the same workflow for midi.
You will need to add a new midi track and select the input device. Keep in mind that the V-drums use channel 10 by default, the same as most midi percussion sets.
Then record the midi track as you would audio. This will capture the note events independently of the drums sounds used for playback.
There are plenty of good midi controlled drum kits (your V-Drums are a hardware example). For the simplest software based approach you will want to use VSTi (VST Instrument) plugins. These implement synthesizers, samplers, and combinations of the two.
Since VST has been around for a while now there are plenty or free plugins available to get you started. Some of the included limited, but very usable, versions of commercial instruments.
Here are just a few of the sites available:
In my experience one of the simplest high quality instruments to start with is SampleTank FREE. When you are comfortable with the process you may want to try out a other samplers like Battery.
Hope that gives you jump start.