DBs run side by side and are simply backed up regularly with whatever backup solution the VPS offers.
That's it.
Out of school I put way more effort in building my infrastructure but in reality a good VPS, something like Cloudflare and some app based caching can run millions of daily views over 20+ different apps without issues.
Edit:// it's mostly rails apps I host btw. For my wordpress installs i use dedicated VPSes because those scale horrible.