Autoupgrading Prestashop is a pain in the ass. The best guide I have found to upgrading Prestashop can be found at http://www.prestashop.com/forums/topic/136668-autoupgrade-guide/ but be warned, it stands at 38 pages as of 2nd November 2012. The best thing to do is to search of your error within the topic.
The link for the free Prestashop AutoUpgrade Module (currently version
0.34 0.93) is: http://addons.prestashop.com/en/administration-tools-prestashop-modules/5496-autoupgrade.html.
The module is very experimental but I found one of my sites that I ran the module upgraded without any problems (from version 22.214.171.124 to 126.96.36.199).
Always remember to carry out a manual backup first and check what files are going to be overwritten.