I got an organ track that was originally a straight organ performance with no rotary speaker applied.  I invoked the plugin and it has a fast/slow switch or selection that I can use in real time, but I would like to automate it or even manipulate it in real time by clicking on the the fast/slow button while it records itself onto a new track.  How is this done?  Is there an easier way to use automation?  I hope that I wasn't too unclear...
 
Regards

Generally you can record the fast / slow as controller data.
Consult help or wait for a reply from someone smarter. That's all I got.
 

This is a previously recorded audio track and I was wanting to use an audio effect in real time.  I sort of stumbled across a method that seemed to work for me. I added the rotary organ effect, selected it in the track's edit filter "fast/slow" switch, clicked on the automation write button, and started the track from the start.  While it played, I clicked the fast/slow switch when I wanted it to go fast or slow and it recorded it.  When I played the track back, it switched where I had made the changes.  I also noticed that I didn't have to use the main track's record button.  It appeared to record the changes through the automation write button.  Is this how it's generally done? Or, is there a better way?

I put the effect plugin into the effect bin from the track.
Then I select the clip(s) and apply the effect to the clip(s). Menu: Process -> Apply Audio Effects.
This is working with or without automation.

There are other ways to do it, but the way you did it is just fine.

It seems tailor made for use of an aux track.

I'd just automate the plugin like you did. I don't understand why you would need to "rerecord" it, you can just leave the plugin on. If you do, for some reason, need to print the effected sound to audio, as John said you can use an aux track.

digimidi
This is a previously recorded audio track and I was wanting to use an audio effect in real time.  I sort of stumbled across a method that seemed to work for me. I added the rotary organ effect, selected it in the track's edit filter "fast/slow" switch, clicked on the automation write button, and started the track from the start.  While it played, I clicked the fast/slow switch when I wanted it to go fast or slow and it recorded it.  When I played the track back, it switched where I had made the changes.  I also noticed that I didn't have to use the main track's record button.  It appeared to record the changes through the automation write button.  Is this how it's generally done? Or, is there a better way?

You can route the rotary effect to an AUX track, click record on the AUX and manually operate the effect. 
OR
You can create 2 AUX tracks.  On one record the fast rotary in a single pass, the other AUX, a slow rotary pass.  Once both recorded, edit the printed wave files.
HOWEVER,  this second option will not allow for that cool sound when a real Leslie goes from fast to slow or slow to fast.  There is that ramp up and ramp down sound you get. 
 

Thanks for the replies.  I guess I'll continue to use the method I described above that was successful for me as well as the aux track.  Re-recording it as I originally thought is now known to me to be an inferior method which I will avoid like the plague.

As a follow up question, you asked if there was an "easier" way to do automation. Was there anything you could conceive of being faster? The only thing I figured you maybe did "extra" was select the fast/slow switch in the track edit filter. You don't need to do that - just enable automation recording and click away at the plugin. It seems really straightforward to me. Were you hoping to draw in the switches with a pencil too or do it some other way?