Go to WordPress Dashboard Add/Edit Page/Post where you have used [allcity] shortcode and you can find metabox like below.
Here you can Add city/country as per your site requirement .Also you can Edit/Delete your city/country.
You can also manage city/country listing that are default available in WPLocalPlus-Int plugin.
Go through WordPress Dashboard -> WPLocalPlus Intl -> Allcity Management
Enable check box of country name which you need to display on site . Also you can enable city name in selectbox which you need display on your site .
Click on Update button to save your changes.