Hi John,
When using the `#pix` helper to get the logo, yes it will rely on the image as provided in the theme. This improves caching of icons (eg. up and down arrows etc.) and is widely used throughout the site.
After uploading a logo through Ventura or Basis theme settings (I'm assuming you're trying on t12 or above here), the URL for the logo can be retrieved using `logourl` in `totara_core\masthead_logo` template, or by providing`$PAGE->theme->setting_file_url('logo', 'logo');` to your mustache template. For an example (including fallback code in the case where the setting is not set), have a look at the `export_for_template` method in `server/totara/core/classes/output/masthead_logo.php` (TXP13+).
PS. Don't forget the alt text so that a screen reader user knows what the logo is (`logoalt` in the masthead template or `$PAGE->theme->settings->alttext` from PHP).
Kind regards