From the perspectives of Schema.org, JSON-LD, and search engines like Google, placing the markup in Header or Footer of your site should not matter.

You can place schema.org json-ld markup anywhere on your page.

JavaScript notation embedded in a <script> tag in the page head or body. The markup is not interleaved with the user-visible text, which makes nested data items easier to express, such as the Country of a PostalAddress of a MusicVenue of an Event. Also, Google can read JSON-LD data when it is dynamically injected into the page’s contents, such as by JavaScript code or embedded widgets in your content management system.

Google

Schema Markup Output

Schema Premium plugin have setting to control where you want to output schema.org markup, you can find under the advanced settings:

Schema Premium Advanced Settings
Advanced Settings

In Schema Settings Advanced tab, you will find the option to select where to output the markup, you can select between

  • Head
  • Footer

The default setting is: Head.