Please excuse my generic~ness, I don't have all the security in place yet.

shop/includes/configure.php
Code:
  define('HTTP_SERVER', 'http://www.mydomain.com');
  define('HTTPS_SERVER', 'https://www.mydomain.com');

  define('ENABLE_SSL', 'true');

  define('DIR_WS_CATALOG', '/shop/');
  define('DIR_WS_HTTPS_CATALOG', '/shop/');

  define('DIR_WS_IMAGES', 'images/');
  define('DIR_WS_INCLUDES', 'includes/');
  define('DIR_WS_FUNCTIONS', DIR_WS_INCLUDES . 'functions/');
  define('DIR_WS_CLASSES', DIR_WS_INCLUDES . 'classes/');
  define('DIR_WS_MODULES', DIR_WS_INCLUDES . 'modules/');
  define('DIR_WS_LANGUAGES', DIR_WS_INCLUDES . 'languages/');
  define('DIR_WS_DOWNLOAD_PUBLIC', DIR_WS_CATALOG . 'pub/');
  define('DIR_WS_TEMPLATES', DIR_WS_INCLUDES . 'templates/');

  define('DIR_WS_PHPBB', '/path_to/board/');

  define('DIR_FS_CATALOG', '/path_to/shop/');

  define('DIR_FS_DOWNLOAD', DIR_FS_CATALOG . 'download/');
  define('DIR_FS_DOWNLOAD_PUBLIC', DIR_FS_CATALOG . 'pub/');
  define('DIR_WS_UPLOADS', DIR_WS_IMAGES . 'uploads/');
  define('DIR_FS_UPLOADS', DIR_FS_CATALOG . DIR_WS_UPLOADS);
  define('DIR_FS_EMAIL_TEMPLATES', DIR_FS_CATALOG . 'email/');
....
shop/admin/includes/configure.php
Code:
define('HTTP_SERVER', 'http://www.mydomain.com');
  define('HTTPS_SERVER', 'https://www.mydomain.com');
  define('HTTP_CATALOG_SERVER', 'http://www.mydomain.com');
  define('HTTPS_CATALOG_SERVER', 'https://www.mydomain.com');

  define('ENABLE_SSL_CATALOG', 'true');
  define('ENABLE_SSL_ADMIN', 'true');

  define('DIR_WS_ADMIN', '/shop/admin/');
  define('DIR_WS_CATALOG', '/shop/');
  define('DIR_WS_HTTPS_ADMIN', '/shop/admin/');
  define('DIR_WS_HTTPS_CATALOG', '/shop/');

  define('DIR_WS_IMAGES', 'images/');
  define('DIR_WS_ICONS', DIR_WS_IMAGES . 'icons/');
  define('DIR_WS_CATALOG_IMAGES', HTTP_CATALOG_SERVER . DIR_WS_CATALOG . 'images/');
  define('DIR_WS_CATALOG_TEMPLATE', HTTP_CATALOG_SERVER . DIR_WS_CATALOG . 'includes/templates/');
  define('DIR_WS_INCLUDES', 'includes/');
  define('DIR_WS_BOXES', DIR_WS_INCLUDES . 'boxes/');
  define('DIR_WS_FUNCTIONS', DIR_WS_INCLUDES . 'functions/');
  define('DIR_WS_CLASSES', DIR_WS_INCLUDES . 'classes/');
  define('DIR_WS_MODULES', DIR_WS_INCLUDES . 'modules/');
  define('DIR_WS_LANGUAGES', DIR_WS_INCLUDES . 'languages/');
  define('DIR_WS_CATALOG_LANGUAGES', HTTP_CATALOG_SERVER . DIR_WS_CATALOG . 'includes/languages/');

  define('DIR_FS_ADMIN', '/path_to/shop/admin/');
  define('DIR_FS_CATALOG', '/path_to/shop/');

  define('DIR_FS_CATALOG_LANGUAGES', DIR_FS_CATALOG . 'includes/languages/');
  define('DIR_FS_CATALOG_IMAGES', DIR_FS_CATALOG . 'images/');
  define('DIR_FS_CATALOG_MODULES', DIR_FS_CATALOG . 'includes/modules/');
  define('DIR_FS_CATALOG_TEMPLATES', DIR_FS_CATALOG . 'includes/templates/');
  define('DIR_FS_BACKUP', DIR_FS_ADMIN . 'backups/');
  define('DIR_FS_EMAIL_TEMPLATES', DIR_FS_CATALOG . 'email/');
  define('DIR_FS_DOWNLOAD', DIR_FS_CATALOG . 'download/');
....