[Manal]

You use seperate vHosts per site and give each site its own TLS certificate (I recommend Let's Encrypt since it is free and supports Wildcard). Or what exactly is your question? Like how to actually setup the whole web server, etc. plus installing your website scripts?

This can be good. But doing so will require you to keep a checklist of stuff you're doing, for which, you need to be kinda "intermediate" at this level.
Alternatively, you can use CyberPanel(I use it for my clients requiring to run big stuff on their VPS and don't have much time to keep a checklist).