If you want to change some settings for alls ites, then edit the vhost config template file in /usr/local/ispconfig/server/conf/. If you want to add settings for one site, then add them in the nginx directives field on the options tab of the website.
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I did purchase the manual, but unfortunately I was not able to find the information I actually need.
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The nginx directives field is described in the manual on page 101.