The words you are using scare me, so let me go ahead and make you a list...
1. Back up your phpbb root folder. Deffintaly first thing incase something goes wrong.
2. Download the new phpbb
3. FTP into server and upload everything except the contrb and install folder and the config.php file.
4. When the first file that goes to upload thats already on the server ex..you upload index.php and you already have index.php on the server, you click overwrite. The only file being effected at that moment is index.php. Once its done upload the new file, whenever someone goes to www.yoursite.com/phpBB/index.php
itll show the new file instead of old one. And as you go along overwriting each file then itll do the same thing.
Now, that is just if you want to return to the old style, but unforutnatly it doesnt delete any files you may not need. Other options would be to back up then delete everything except the phpbb/config.php file or maybe even upload the new phpbb as phpbb2, delete the contrib and install files, replace the config file with the one from the server, then rename the original phpbb folder to something else and then rename phpbb2 to the original phpbb name. Then delete the old php folder. (Hope that makes sense)