There are five very important simple steps:

1. Make sure your sequencer is set to receive input from the Virus.
2. With the Virus Arpeggiator Send (CTRL -> MIDI -> ArpeggSend) set to "Off" record the notes you wish to trigger the arpeggiator with onto a track (let's say MIDI channel 1).
3. Now set Arpeggiator Send to "On" in the Virus and make sure the sequencer is setup to receive input from the Virus.
4. Create a new track set to a different channel with a non-arpeggiated patch on the Virus (let's say MIDI channel 2) and press record.
5. Now after the track plays to completion, mute track one and track two should contain the individual notes.
It is important to use a different patch and MIDI channel for the second track to avoid the dreaded MIDI loops that will occur otherwise. And while it seems logical enough...make sure you have MIDI cables connected to your ins and outs!