Whilst this probably would be better suited to Server Fault, I guess it's good practice for webmasters. Here's a webmasters take on your question...
A few points:
Give advance notice. It's common courtesy and especially important on an e-commerce site. (Imagine spending hours filling a cart, only to have it all lost when some mug decides to restart apache.)
If possible, do a dry run first. Try out your planned changes on a local version of your server. This will save you from being offline for longer than necessary and will mean that any problems can be fixed in a low-stress setting.
Make backups!cp php.ini php.ini.bak only takes a few seconds and can save your ass if you botch things. No matter how trivial the modification, make a backup. And don't delete/overwrite it until everything's been thoroughly tested. (I personally keep stable versions indefinitely.)
Identify if there's a quiet time across all your sites. If all your e-commerce sites are targeted at users from one country, there'll probably be a quiet period in the early hours of the morning. Updating your server configuration will usually involve some downtime, even if it's just a few seconds, so time your update to annoy as few people as possible.