There is absolutely no need to change the way ispconfig handles subdomains as you just created the subdomain the wrong way. If you like to have a separate directory for a subdomain, you simply click on new website, enter sub.domain.com into the domain field and click on save.
If you want to test a website before you put it in production, you just click on new website, enter test.cdomain.com into the domain field and click on save. If the site shall go live, you edit the website settings and change test.domain.com to domain.com abd click on save. Thats all.