That's no way to think about handling a production server.
I'm not experienced with the Zend Server product, but I wouldn't just install anything on top of a running production system.
Instead, get yourself a new server that will eventually replace your production server.
Then:
- Start with a clean install of your distro of choice.
- Install ZS (take notes on exactly what you do)
- Install your application and data (take notes on exactly what you do)
- Test it thoroughly.
- If it works, nuke the server, and repeat 1-4, using your notes.
Once you're satisfied that you can get everything working "from scratch" using your notes, create a plan to migrate from the old server to the new one.
Doing it this way ensures that
- You have minimal downtime.
- You don't have some mess with ZS installed over the top of some other set up.
- You can re-build your server when necessary (you created documentation)
2016 Edit: These days, there are various tools such as chef, ansible, or salt that replace obsessive note-taking with automation. I highly recommend anyone managing production systems learn one or more and use them liberally.