Copying Content vs. folders

I installed WordPress 2.3 from GoDaddy, and now need to update to 2.3.1. I will be using ftp to upload the new files. How do you recommend doing this? The 3-Step Upgrade in WOrd Press’ docs gives the cautionary statement:
“The wp-content folder requires special handling, as do the plugins and themes folders. You must copy over the contents of these folders, not the entire folder. Copying the entire folder overwrites all your customizations and added content.”

Does this mean that I need to identify and compare each folder and subfolder that I’ve downloaded and then go back and forth between my download and what is on my hosting server and ftp only individual files from each downloaded folder into the same folders on my hosting sites servers?

Seems like a lot of back and forth, and lots of room for error.

KBerTy