each site gets it's own nginx config file, domain.name.conf (replace domain.name with real domain)
databases get prefixed with the domain name (replace . with _ )
Also, I'm working on a script to handle the DNS zones for me.
Also, I'm working on a script to handle the DNS zones for me.
Yeah, we worked on one of those, too. We called it Webmin (literally, Webmin began as a simple tool for managing and delegating management of DNS records about 14 years ago). And, then we worked on a script to manage virtual hosts, mailboxes, databases, web applications, LDAP, DNS slaves, SVN and git, awstats and Webalizer, resource usage data collection and reporting, user management and delegation to untrusted users, virus and AV scanning, Greylisting, SPF record management, DKIM key management, automated backup and restoration of virtual hosts and all associated data, etc. We called that script (or huge pile of scripts as the case may be) Virtualmin.
Again, I encourage you to work in whatever way you are most comfortable and productive. I manage a few dozen websites, and find having tools to automate much of that process is valuable for me. Millions of users seem to agree that Webmin and/or Virtualmin removes tedium for them, as well. And, I'm sure the same can be said of cPanel users.
Incompetence is not the only reason someone would do something differently than you. Different requirements breed different solutions.
If that's too much, you don't need to use it. (You could shut it down when you're not using it, though it loses a lot of its utility when it can't communicate with your slave DNS servers, keep resource usage data, etc.)
Virtualmin is a more complicated beast, and can take quite a bit more memory, if caching is enabled, but that is optional, and when disabled it takes the same ~11MB as Webmin.
You can no more build a full-featured virtual hosting stack with email (and spam/AV scanning), web, databases, mod_fcgid or fastcgi with suexec, DNS, etc. in 64MB without a control panel than you could with a control panel. Likewise, if you just want web service, you can build one with Virtualmin in X+11 MB of RAM (where X is the amount of RAM the system and web server require).
Of course, Virtualmin (or cPanel or Plesk) are not targeted to very small deployments. They're for shared hosting, which tends to be on a larger system where a few MB for the control panel is of negligible impact.
I just want it to be clear that "control panel == memory hog" is not really accurate. It's probably all the stuff that users expect from a control panel-equipped system that makes it require more memory. ClamAV, for instance, requires more than 200MB. MySQL for a single moderately popular website can consume 300MB. Apache can grow as big as your imagination, because there are so many modules people can enable. A thoroughly stripped Apache isn't all that big, but the average Apache process is a couple hundred MB.