The way I always do it....I slide the effect output to off with automation turned on. For example, say I'm using like a Sonitus delay and want my vocals to have delay in certain spots.
I turn on automation, select the level I want the delay to be at, press play and then just turn the effect output slider to 0 in the passage where I don't want delay.
Then while still playing back, hit "undo" to bring it back to my delay level I want, then hit undo and it will go back to 0. Press stop and my automation is complete. If there is something I need to fix, I go back and adjust the nodes accordingly. Sometimes I rehearse my "undo" procedure to get it down tight. Other times I nail it on the first try. It's not the ideal way to do things, but it works perfectly for me. :)
-Danny