There are currently 2 ways to manage your folders. You can double click on the folder names on the left feed list and rename. This will work on everything except the “Subscriptions” folder, which you cannot change/remove.

The second way is through the subscriptions management page here: https://theoldreader.com/subscriptions

In this interface, instead of renaming folders, you can move all the feeds from the folder you want to rename to a new folder.