When I try to add a domain as a new web site or add a domain with dns or email the drop down box gives me a list of domains. How do I add a new domain to the list? I need to add a domain to make sure ispconfig is writing to disk.
Writing to disk happens after any change, it does not have to be domain. My guess about the domain list is you are not logged in ISPConfig as admin, but a customer account. And there is turned on the setting "Use the domain module to add new domains" in Domains tab under System Config. See ISPConfig Manual 3.1 page 290. So to add domains to that drop down list, admin adds the domains for the customer.
Likje @Taleman mentioned you have the domain module enabled when the domain field is a drop-down. When the domain module is on, then Domains must be added in client module first. If you don't want to use this feature, then disable it again under System interface config. Btw. Domain Module is off by default, so you must have enabled it manually after install.