//Here are my fields for the post_meta in my cpt

    <p>
      <span class="project-types-row">Project Type(s)</span>
      <div class="project-types-row-content">
          <label for="meta-checkbox">
              <input type="checkbox" name="project-types-sactivity-checkbox" id="project-types-sactivity-checkbox" value="yes" <?php checked( $mtp_project_stored_meta['project-types-sactivity-checkbox'][0], 'yes' ); ?> />
              Student Activity
          </label>
          <label for="meta-checkbox-two">
              <input type="checkbox" name="project-types-sorganization-checkbox" id="project-types-sorganization-checkbox" value="yes" <?php checked( $mtp_project_stored_meta['project-types-sorganization-checkbox'][0], 'yes' ); ?> />
              Student Organization
          </label>
          <label for="meta-checkbox-three">
              <input type="checkbox" name="project-types-sproject-checkbox" id="project-types-sproject-checkbox" value="yes" <?php checked( $mtp_project_stored_meta['project-types-sproject-checkbox'][0], 'yes' ); ?> />
              Student Project
          </label>
          <label for="meta-checkbox-four">
              <input type="checkbox" name="project-types-torganization-checkbox" id="project-types-torganization-checkbox" value="yes" <?php checked( $mtp_project_stored_meta['project-types-torganization-checkbox'][0], 'yes' ); ?> />
              Teacher Organization
          </label>
      </div>
    </p>


//and here I check for input and save

    if( isset( $_POST[ 'project-types-sactivity-checkbox' ] ) ) {
      update_post_meta( $post_id, 'project-types-sactivity-checkbox', 'yes' );
    } else {
        update_post_meta( $post_id, 'project-types-sactivity-checkbox', '' );
    }

    if( isset( $_POST[ 'project-types-sorganization-checkbox' ] ) ) {
      update_post_meta( $post_id, 'project-types-sorganization-checkbox', 'yes' );
    } else {
        update_post_meta( $post_id, 'project-types-sorganization-checkbox', '' );
    }

    if( isset( $_POST[ 'project-types-sproject-checkbox' ] ) ) {
      update_post_meta( $post_id, 'project-types-sproject-checkbox', 'yes' );
    } else {
        update_post_meta( $post_id, 'project-types-sproject-checkbox', '' );
    }

    if( isset( $_POST[ 'project-types-torganization-checkbox' ] ) ) {
      update_post_meta( $post_id, 'project-types-torganization-checkbox', 'yes' );
    } else {
        update_post_meta( $post_id, 'project-types-torganization-checkbox', '' );
    }