Not so, you just add an increment to the shortcode, as outline in the FAQ –
Q – Can I use this plugin to place more than one iframe in a page or post?
A – Yes. As many iframes can be embedded in a page or post as you may want. Just increment the field name, say from iframe1 to iframe2, iframe3 … iframeX. For example if you wanted three iframes in the page your short codes could be [field name=iframe1] [field name=iframe2] [field name=iframe3] and then in the Name section of the Custom Fields area you would have one for each short code. So one line would have Name = iframe1 Value = < your iframe code > and so on as needed.