Depends on why you are running it. If you are running it to update a configuration you've updated in the context file, you might not see the configuration updated until you bounce the apps tier.
It's not mandatory to stop application before running the autoconfig; you can run autoconfig anytime but it will not affect until you bounce the application.
Normally steps are as follows -
1. stop the application
2. run autoconfig
3. Start the application
or if you can't stop the application and run autoconfig, because it it time consuming and you don't want to spend that much time. We normally follow below steps -
1. run autoconfig
2. bounce the application
I am using autoconfig for cloning.
Can I run autoconfig and then preclone, then copy clone without bouncing the apps?
Yes you can. This is the right way.