Here you are, your website is all done, launched and you have a stream of visitors stopping by on a regular basis. Great! That hard work of adding in all these plugins, special themes, some custom code – it’s all paying off finally. Then one day you login and there’s that yellow upgrade notice. Or a plugin or twenty has an upgrade notice. And now the theme framework has one too.
With all the moving parts in one install, yes that does mean there is an increased risk of something breaking whenever one of those parts gets upgraded. You can mitigate those risks, however.
1) Backup. Every time you upgrade anything, you have to do a backup first. This way, in a worse-case scenario, you can put things back the way they were. Backups are your backup plan. The critical areas are your database(s) and the wp-content folder. How to manually backup wordpress mu.
2) Do your homework. Check the various support forums for each component that needs upgrading and see if there have been any reported problems. Part of lessoning the fear & panic is knowing what to expect, especially the pitfalls.
3) Relax & remain calm. The worst time to upgrade is late at night or when you are in a hurry. Mistakes can be made far more easily then, and if something does go wrong, you’re likely to be more stressed & overtired. (unless you work well at night, as some do) If you’ve made your backups & have support forums threads open in other tabs in your browser, then you know you can manage.
4) Wait. I’m not suggesting to delay critical upgrades indefinitely, but you can usually afford to wait a week when it’s more convenient to do upgrades on a number of plugins & themes & core, than spread out. You could spend every other day upgrading something if you clicked the links every time they showed up.
For extra credit: while WordPress & MU make it clickably easy to upgrade from the backend, another skill used in fixing messed up upgrades is knowing how to do them manually. Some of us rarely use the internal upgrade process, preferring manual control. The brief version of this is simply replacing the files on the server with new copies.