You'll need a registered version of Titanium Backup. If you haven't bought it already I really recommend it, it's the single most useful app I've had on android. Go into the backup/restore tab, scroll down and find the app that you updated. It'll be listed in red, meaning it's a /system app, but it'll say (update) next to it, indicating the update is on the internal storage. Long press it, and there will be an option that says something like "move update to /system" or similar. Press that, and it will remove the original version from /system, and move the update in it's place.
You can also move apps to /system this way, long press any normal app and there's an option for "convert to system app" that will move it over. I deleted a lot of the bloat apps, as well as all of the default ringtones, and had plenty of free space to move some of my most-used apps over to /system.
Right now, I have 26.1 MB free in /system, 60.5 MB free in /data, and something like 300 MB worth of apps on my second SD card partition.