Manual:$wgUploadDirectory

Uploads: $wgUploadDirectory
The file system path of the upload directory.
Introduced in version:	pre 1.1.0
Removed in version:	still in use
Allowed values:	absolute path
Default value:	"{$IP}/images" "{$IP}/upload" prior to 1.8.0 (Note: The default value of this variable depends on other variables, such as the values set in Setup.php, after LocalSettings.php is executed)

Other settings: Alphabetical | By Function

Details

The file system path of the folder where files will be uploaded. If one wants to have separate resources folder per wiki yet sharing same source code then it can be changed to below in their corresponding LocalSettings.php file.
$wgUploadDirectory = "{$IP}/images/wiki1";

$wgUploadDirectory = "{$IP}/images/wiki2";

Note: There are other variables which are defined relative to this one. If you redefine this in your LocalSettings.php then all dependent variables including $wgUploadPath will need redefining also. If both these settings are not coherent the files will be uploaded to different folder ($wgUploadDirectory) than from where MediaWiki will try to retrieve it for viewing ($wgUploadPath)!