If you copied the files from their previous location, you need to edit the config.inc.php file and the three config.core.php files (root, manager, and connectors directories) to point to the new location.
Be sure you delete all files in the core/cache directory before running setup, and again whenever you make a change to the config files.
If you copied the .htaccess file to the subdirectory, it may need to be modified or temporarily renamed.
Since you are moving the site, your browser cache or cookies could also be an issue.
Once you get the Manager working, make sure the base href tag in all templates looks like this (with the exclamation point):
<base href="[[!++site_url]]" />