What are best practices for configuring a server for WordPress sites?

I hired a sysadmin to set up a VPS server for me and, unfortunately, it looks like things were not set up correctly. When trying to install and update plugins, I run into permissions errors all the time. WP Super Cache is the main issue as it causing my readers to run into 502 errors. Currently, my site does not load pagination (no Page 2, Page 3, etc..).

How do I transition multiple installations to a single Multisite installation?

I have a client who runs 8 different blogs, currently on 8 separate installations of WordPress. I’m trying to encourage them to move to a single MS installation instead to make it easier (mostly on me) to maintain the different sites, themes, and mix of plug-ins. Unfortunately, I shied away from MU for the longest time, and now I have no idea where to start with MS.