When creating a new site it has a default index.html and and error folder. Where do these files originate? I would like to change it to something else.
These originate from /usr/local/ispconfig/server/conf/index/ and /usr/local/ispconfig/server/conf/error/. You should place the modified files in /usr/local/ispconfig/server/conf-custom/index/ and /usr/local/ispconfig/server/conf-custom/error/.