If I'm using an amp sim plugin on a track, set up with a distortion tone, is there a simple way to record a clean part on the same track, disabling the amp sim for only the desired part(s), just as you would switch between clean and distorted channels on a real amp?
 
Or am I better off using two separate tracks for each tone?
 
What are your methods?

I just use 2 tracks. I suppose you could make it a stereo track and record clean and processed to left and right channels, but I think it's easier to just record 2 tracks personally. Plus it's easier to do any downstream processing that way. You can just Comp the two parts to go back and forth.

Definitely 2 separate tracks.
 
You might find you'll need to phase align them, this is much easier when dealing with 2 separate tracks

When I use GR5 for full sim, it's monitors effected but records dry.  I bounce to track to get the effects printed while retaining the clean track.  From there I slice/mute the two tracks to get what you described.
 
You can use a foot controller (or any controller really) to control GR5 just like a regular amp's footswitch and record that way too.
 
With the dry track, you can always drop a copy on another track and use a different sim, or even route external for proper reamping.

I'm pretty sure that the amp sim is not recorded at all; the effect is on the output only. To permanently add the effect to a track you would have to bounce or Process>Apply FX.
But, using automation on the amp sim (if it is automatable), you could turn the effect on and off in the same track and it should play back as you set it.

Yes, SONAR records all tracks dry.

57Gregy has it. What you're recording is the dry signal.

That said, the dry signal is not what you'll want for a "clean" tone. Straight pickup tone is not really anything like a clean amp tone. You want to be switching settings on your amp sim, not switching it on and off.

Thanks for the responses, all. Looks like just using separate tracks is probably the way to go.
 
 

57Gregy
But, using automation on the amp sim (if it is automatable), you could turn the effect on and off in the same track and it should play back as you set it.

 
That's the one possibility that I had considered, but wanted to see if there might be any other ways that I was overlooking.
 
Probably just easier to create another track, especially when you throw another amp sim into the mix for a good clean tone, as John was getting at.