Of course overwrite it. If you place the new forum in a different folder then search engines will have to crawl a completely different URL, and it will take some time for your forum to get earn back its reputation in search engines.
Also as you haven't yet converted, let me tell you, vBulletin's SEO is better than IPB's so far as I know.
Another thing, many a times owners lose data while converting forum softwares, like often user passwords are lost and everyone has to reset their passwords, so its certainly a drawback.
Anyways, Good Luck with your forum