Hosting multiple websites in one account can be tidy if each site has clear boundaries. Without organisation, it becomes hard to maintain and risky to migrate.
Separate Document Roots
Each site should have its own document root. Do not place one live site inside another site's public folder.
Name Things Clearly
Use obvious names for databases, users, folders, and cron jobs. Future maintenance becomes much easier.
Keep Backups Separate
Know which backup belongs to which site. A restore should not accidentally overwrite the wrong project.
Review Access
If different developers work on different sites, avoid giving everyone access to everything.
Multiple sites are manageable when structure exists from the start.