I installed drupal 7.9 and commerce kickstart about a month ago.

In the meantime as well as core, commerce offers a new version.
Autoupdate cannot update commerce (core is allways manual, I know).

After kickstart has the modules in the package folder, update does not find them.

But if you move the modules to site/all/modules, commerce does not work anymore, becaues kickstart somehow is modified for this special installation path.

How do I get out of this trapp?

After the shop is not built yet, I can change installation sheme.
But when this is done, and when I inserted roundabout 10.000 Products, I cannot play with this anymore.

This is, why I want to get it right from the beginning.