My website uses nginx. I personally use apache just for large file uploading towards the server. I've got a script upload.php that we Publish the files to using a expensive uploader script.

Apache operates on a subdomain, and so i publish files to upload.domain.com/upload.php

Can there be in whatever way to avoid apache from serving the particular site on that subdomain? ideally I wish to publish files to upload.subdomain.com and also have it's forwarded to upload.php on that subdomain

I am talking about I possibly could setup another document root for apache and thats it, but are there more ways?

Basically understand properly you would like all demands to upload.domain.com to become forwarded to upload.php? A RewriteRule within the VirtualHost that catches all demands should work:

RewriteEngine On
RewriteRule .  /full/path/to/upload.php