Hmm best would even be (especially for a fresh start) to rename your current vB directory, then create a fresh one for 3.6, upload 3.6, copy over config.php (and other things that you might need) and run upgrade. If all go wrong, you can simply delete 3.6, rename the old directory back and restore database.
I would always advise to first create a testboard to test the process and make sure you have backups for both database and file system for each "milestone" in your upgrade.
PS Good reading might be
eva2000's Upgrade method
PS Going to move this to vBulletin discussion because it is not really a coding topic but more general.