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.
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:
In Schema → Settings → Advanced tab, you will find the option to select where to output the markup, you can select between
The default setting is: Head.