Can my Fantom X6 be integrated into Sonar like a virtual instrument???

Get an instrument definition file for the Fantom, if SONAR doesn't come with one already. What that does is map the synth's patches so you can select them easily from dropdown listboxes within SONAR, just as easily as you would with a soft synth.

If you record your performances as MIDI rather than as audio, you'll then have options you wouldn't have after simply recording audio directly. You can edit the part, throw out accidental double-notes, tighten timing, try out alternate patches. When you're ready to commit to audio, you can either drive the Fantom from the MIDI track or substitute another synthesizer. 

I'd suggest recording audio over S/PDIF (as opposed to the audio outputs) for maximum quality.