Rewrite new URLs only

I have yet to install vbseo and already have lots of URLs crawled by Google.
Once I install it, is there a way I can use the URL rewrite feature on new threads only and leave old forum threads using vbulletin's default URL structure?
In the case I need to rewrite all of my URLs, will my rankings be affected for a while because of the new URL structure?

No, it will make all the vBSEO styled URLs. However, all of your traffic will be 301ed (redirected permanently) to the new URL vBSEO URLs.

Is it true that my rankings will be affected for some time by this change?

Yes, you might see a negative drop after installing, which is the transition of removing the old URLs to the new URLs.