The WordPress Plugin "Popups - WordPress Popup" supports more than one pop-ups.
After you install and activate the "Popups - WordPress Popup" plugin, a new item named "Popups" will appear in the WordPress Dashboard.
Please create a new pop-up by clicking "Add New". If you create several pop-ups, you need to specify the box position for each pop-up in order not to be overlapped.
The "Box Position" option can be set under the section "Display Options."
You can also set other options including "Cookie expiration days."
The following examples shows two pop-ups: