I'm attempting to upgrade from 1.3.9b to the current version. Here's what I've done:

Made a copy of my live site (both files on webserver and database) so I'm working with a fully working copy of the store at /storecopy/ (original site lives at /store/)

Uploaded the 1.5.1 update over the top of /storecopy/, choosing to overwrite in all cases

Ran the install procedure, updating /storecopy/'s copy of the database to 1.5.1

Here's where I'm getting confused: When I tried to access storecopy/admin, I got an error message telling me I couldn't access /admin without changing the name of the admin folder. I did that following the instructions linked, which said (since I was on 1.5.1) all I needed to do was change the folder name. When I did that and tried to navigate to storecopy/mynewadminfoldername, I got my webhost's 404 page. But when I made the necessary changes to /storecopy/mynewadminfoldername/includes/configure.php (as if I was still running on 1.3.9b), it worked.

So my question: Why? Are the instructions wrong, or have I done something wrong so far? Do I need to make those changes in includes/configure.php, or no?