The GitLab One-Click image uses the "Omnibus" installer. It ships its own bundled version of Nginx, and is designed to be stand-alone. The there are ways to tweak it. You'll want to take a look at the README for GitLab's "Omnibus" installer especially this doc on Nginx settings for GitLab.

Your best bet is probably to add a custom Nginx "server block." This will allow you to set up a separate Nginx config file for for In /etc/gitlab/gitlab.rb add:

external_url "http://example.com"
nginx['custom_nginx_config'] = "include /etc/nginx/conf.d/*.conf;"

You can now create a server block for your main site in the /etc/nginx/conf.d/ directory. Then run gitlab-ctl reconfigure to pick up the changes.

Check out some of the tutorials under the Nginx tag for a better understanding of the way to set up the configuration. It will depend on what kind of scripts you are trying to run.