Upgrading directory query

[tosd]

After reading the upgrade instructions I was surprised to see that it seems to be assumed that the existing installation of Prestashop will be in a sub-directory (http://www.mysite.com/prestashop/). Is this normal? I would have thought that many installations would be in the root directory - mine certainly is.

I have tried downloading a backup - deleting the online version from the root directory - transferring the 1.2.3 version to the root in place of the old one and then updating image folders/modules etc from the original version and setting permissions as per instructions. So far though I have had no luck at all. The install function just gets stuck as so many others have reported several steps in.

Is the fact that I have Prestashop installed in the root directory likely to be part of my problem?

Any helpful advice welcome.