Confusing instructions

I used the ones that were presented first, that outlined back up of the data base and key files, then upload the new WP files, and finally browse to http://your.isp.com/wordpressfolder/wp-admin/upgrade.php

So far so good, I go back and reactivate my plugins – all it fine, and it says V2.0.6

THEN I find totally different instructions for updating which include deleteing directories, and says NOTHING about running upgrade.php

So which is it?

I reminded of a comedy skit where one guy tries to defuse a bomb and the other on reads the directions to do it…

“Now cut the green wire”

*snip*

“But first….”

*Yelling and running away…*